Starting phenix.real_space_refine on Sat Feb 17 23:20:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4e_22666/02_2024/7k4e_22666_neut_updated.pdb" } resolution = 4.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 164 5.16 5 C 13027 2.51 5 N 3415 2.21 5 O 3513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 224": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 409": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20119 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "C" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "D" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4996 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 26, 'TRANS': 593} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'VUJ': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'VUJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.92, per 1000 atoms: 0.54 Number of scatterers: 20119 At special positions: 0 Unit cell: (145.35, 145.35, 127.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 164 16.00 O 3513 8.00 N 3415 7.00 C 13027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 53.5% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.970A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.928A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.519A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 139 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 166 through 172 removed outlier: 3.671A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.649A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.615A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.961A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 4.162A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 4.101A pdb=" N GLN A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.865A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.604A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 313 through 323 removed outlier: 4.890A pdb=" N LYS A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 347 removed outlier: 3.578A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 343 " --> pdb=" O TYR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.926A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.813A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.985A pdb=" N ILE A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.586A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 468 " --> pdb=" O ASN A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 486 Proline residue: A 477 - end of helix removed outlier: 4.122A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 removed outlier: 4.045A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.549A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 removed outlier: 3.932A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 3.773A pdb=" N MET A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY A 579 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 581 " --> pdb=" O MET A 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 607 removed outlier: 3.552A pdb=" N ILE A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 58 through 64 removed outlier: 3.970A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 92 through 101 removed outlier: 3.928A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.519A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 166 through 172 removed outlier: 3.671A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.650A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.615A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.961A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 4.162A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 4.101A pdb=" N GLN B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 removed outlier: 3.866A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.604A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 308' Processing helix chain 'B' and resid 313 through 323 removed outlier: 4.890A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 347 removed outlier: 3.577A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 401 removed outlier: 3.926A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.813A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 444 removed outlier: 3.986A pdb=" N ILE B 430 " --> pdb=" O HIS B 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 440 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 443 " --> pdb=" O THR B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.585A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR B 467 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE B 468 " --> pdb=" O ASN B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 486 Proline residue: B 477 - end of helix removed outlier: 4.121A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 509 removed outlier: 4.044A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 538 removed outlier: 3.548A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 removed outlier: 3.931A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.772A pdb=" N MET B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B 579 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 581 " --> pdb=" O MET B 577 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 607 removed outlier: 3.552A pdb=" N ILE B 597 " --> pdb=" O TRP B 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 46 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.970A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.928A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.519A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 166 through 172 removed outlier: 3.671A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.650A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 204 removed outlier: 3.615A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.961A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 4.162A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 4.101A pdb=" N GLN C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.866A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.603A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 308' Processing helix chain 'C' and resid 313 through 323 removed outlier: 4.890A pdb=" N LYS C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.578A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 343 " --> pdb=" O TYR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.926A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 removed outlier: 3.813A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE C 420 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 444 removed outlier: 3.985A pdb=" N ILE C 430 " --> pdb=" O HIS C 426 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 438 " --> pdb=" O PHE C 434 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET C 440 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C 443 " --> pdb=" O THR C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.585A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET C 466 " --> pdb=" O TRP C 462 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE C 468 " --> pdb=" O ASN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 486 Proline residue: C 477 - end of helix removed outlier: 4.121A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 509 removed outlier: 4.045A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 538 removed outlier: 3.549A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 removed outlier: 3.932A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 583 removed outlier: 3.772A pdb=" N MET C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY C 579 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 581 " --> pdb=" O MET C 577 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 607 removed outlier: 3.552A pdb=" N ILE C 597 " --> pdb=" O TRP C 593 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.971A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 92 through 101 removed outlier: 3.927A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.520A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 166 through 172 removed outlier: 3.671A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.650A pdb=" N LEU D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.615A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.960A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 4.162A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 263 removed outlier: 4.101A pdb=" N GLN D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.866A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 308 removed outlier: 3.604A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 303 through 308' Processing helix chain 'D' and resid 313 through 323 removed outlier: 4.890A pdb=" N LYS D 322 " --> pdb=" O SER D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 347 removed outlier: 3.577A pdb=" N TYR D 336 " --> pdb=" O LEU D 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 343 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 401 removed outlier: 3.925A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.814A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE D 420 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 444 removed outlier: 3.985A pdb=" N ILE D 430 " --> pdb=" O HIS D 426 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL D 438 " --> pdb=" O PHE D 434 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET D 440 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 468 removed outlier: 3.585A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL D 465 " --> pdb=" O GLY D 461 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET D 466 " --> pdb=" O TRP D 462 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE D 468 " --> pdb=" O ASN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 486 Proline residue: D 477 - end of helix removed outlier: 4.121A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 509 removed outlier: 4.045A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 538 removed outlier: 3.549A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 566 removed outlier: 3.932A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 583 removed outlier: 3.773A pdb=" N MET D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 579 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 581 " --> pdb=" O MET D 577 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 607 removed outlier: 3.553A pdb=" N ILE D 597 " --> pdb=" O TRP D 593 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 631 through 633 removed outlier: 4.084A pdb=" N VAL A 633 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 631 through 633 removed outlier: 4.083A pdb=" N VAL B 633 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 631 through 633 removed outlier: 4.085A pdb=" N VAL C 633 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 631 through 633 removed outlier: 4.084A pdb=" N VAL D 633 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) 632 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.59 Time building geometry restraints manager: 9.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6330 1.34 - 1.46: 4040 1.46 - 1.58: 9953 1.58 - 1.69: 3 1.69 - 1.81: 276 Bond restraints: 20602 Sorted by residual: bond pdb=" C12 VUJ C 701 " pdb=" C13 VUJ C 701 " ideal model delta sigma weight residual 1.348 1.542 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C12 VUJ D 701 " pdb=" C13 VUJ D 701 " ideal model delta sigma weight residual 1.348 1.542 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C12 VUJ A 701 " pdb=" C13 VUJ A 701 " ideal model delta sigma weight residual 1.348 1.540 -0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" C12 VUJ B 701 " pdb=" C13 VUJ B 701 " ideal model delta sigma weight residual 1.348 1.540 -0.192 2.00e-02 2.50e+03 9.22e+01 bond pdb=" C12 VUJ B 702 " pdb=" C13 VUJ B 702 " ideal model delta sigma weight residual 1.348 1.538 -0.190 2.00e-02 2.50e+03 9.00e+01 ... (remaining 20597 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.30: 582 106.30 - 113.22: 10853 113.22 - 120.14: 7997 120.14 - 127.06: 8253 127.06 - 133.98: 260 Bond angle restraints: 27945 Sorted by residual: angle pdb=" C TYR D 89 " pdb=" N ASP D 90 " pdb=" CA ASP D 90 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C TYR A 89 " pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C TYR B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta sigma weight residual 121.54 130.82 -9.28 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C TYR C 89 " pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " pdb=" CG ARG C 140 " ideal model delta sigma weight residual 114.10 123.18 -9.08 2.00e+00 2.50e-01 2.06e+01 ... (remaining 27940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.54: 11860 24.54 - 49.08: 377 49.08 - 73.63: 33 73.63 - 98.17: 10 98.17 - 122.71: 18 Dihedral angle restraints: 12298 sinusoidal: 5042 harmonic: 7256 Sorted by residual: dihedral pdb=" CA GLN A 230 " pdb=" C GLN A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta harmonic sigma weight residual -180.00 -135.31 -44.69 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA GLN D 230 " pdb=" C GLN D 230 " pdb=" N PRO D 231 " pdb=" CA PRO D 231 " ideal model delta harmonic sigma weight residual -180.00 -135.32 -44.68 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA GLN C 230 " pdb=" C GLN C 230 " pdb=" N PRO C 231 " pdb=" CA PRO C 231 " ideal model delta harmonic sigma weight residual -180.00 -135.36 -44.64 0 5.00e+00 4.00e-02 7.97e+01 ... (remaining 12295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2326 0.061 - 0.122: 689 0.122 - 0.183: 95 0.183 - 0.243: 16 0.243 - 0.304: 12 Chirality restraints: 3138 Sorted by residual: chirality pdb=" CG LEU C 574 " pdb=" CB LEU C 574 " pdb=" CD1 LEU C 574 " pdb=" CD2 LEU C 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CG LEU B 574 " pdb=" CB LEU B 574 " pdb=" CD1 LEU B 574 " pdb=" CD2 LEU B 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU A 574 " pdb=" CB LEU A 574 " pdb=" CD1 LEU A 574 " pdb=" CD2 LEU A 574 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 3135 not shown) Planarity restraints: 3522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 353 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO C 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 354 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 353 " -0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO D 354 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 354 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 354 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 353 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO B 354 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " 0.035 5.00e-02 4.00e+02 ... (remaining 3519 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5763 2.81 - 3.33: 18805 3.33 - 3.85: 32218 3.85 - 4.38: 37730 4.38 - 4.90: 59468 Nonbonded interactions: 153984 Sorted by model distance: nonbonded pdb=" O MET B 578 " pdb=" OG1 THR B 581 " model vdw 2.286 2.440 nonbonded pdb=" O MET C 578 " pdb=" OG1 THR C 581 " model vdw 2.286 2.440 nonbonded pdb=" O MET A 578 " pdb=" OG1 THR A 581 " model vdw 2.287 2.440 nonbonded pdb=" O MET D 578 " pdb=" OG1 THR D 581 " model vdw 2.287 2.440 nonbonded pdb=" OH TYR A 339 " pdb=" O THR A 392 " model vdw 2.311 2.440 ... (remaining 153979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 19 through 638 or resid 701)) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.600 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 53.880 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.194 20602 Z= 0.683 Angle : 1.060 13.788 27945 Z= 0.541 Chirality : 0.058 0.304 3138 Planarity : 0.007 0.064 3522 Dihedral : 12.700 122.709 7610 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 0.56 % Allowed : 6.68 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.12), residues: 2472 helix: -3.35 (0.09), residues: 1224 sheet: -4.24 (0.42), residues: 76 loop : -3.09 (0.16), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 629 HIS 0.007 0.002 HIS D 522 PHE 0.015 0.002 PHE A 523 TYR 0.014 0.002 TYR D 623 ARG 0.004 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1064 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.7566 (p) cc_final: 0.7277 (p) REVERT: A 113 GLU cc_start: 0.9357 (tt0) cc_final: 0.8968 (tm-30) REVERT: A 122 HIS cc_start: 0.9451 (m170) cc_final: 0.9147 (m-70) REVERT: A 123 ILE cc_start: 0.9671 (mt) cc_final: 0.9287 (mt) REVERT: A 136 LEU cc_start: 0.9461 (mt) cc_final: 0.9182 (mt) REVERT: A 146 ARG cc_start: 0.9320 (mtt180) cc_final: 0.8860 (mmm-85) REVERT: A 150 THR cc_start: 0.9184 (p) cc_final: 0.8694 (p) REVERT: A 198 THR cc_start: 0.9662 (t) cc_final: 0.9121 (t) REVERT: A 201 HIS cc_start: 0.9368 (m-70) cc_final: 0.8824 (m90) REVERT: A 215 MET cc_start: 0.9168 (mmm) cc_final: 0.8920 (mmm) REVERT: A 250 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 259 LEU cc_start: 0.9376 (mm) cc_final: 0.9070 (mm) REVERT: A 260 MET cc_start: 0.9593 (tpt) cc_final: 0.9280 (mmm) REVERT: A 263 ARG cc_start: 0.9493 (mmt180) cc_final: 0.9206 (mmp80) REVERT: A 297 ILE cc_start: 0.9309 (pp) cc_final: 0.9004 (tp) REVERT: A 300 LYS cc_start: 0.9002 (mttt) cc_final: 0.8559 (mppt) REVERT: A 306 GLN cc_start: 0.9102 (pt0) cc_final: 0.8680 (pm20) REVERT: A 336 TYR cc_start: 0.9036 (t80) cc_final: 0.8541 (t80) REVERT: A 347 CYS cc_start: 0.9382 (m) cc_final: 0.8345 (m) REVERT: A 403 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8895 (tp30) REVERT: A 406 ASP cc_start: 0.9326 (m-30) cc_final: 0.9114 (m-30) REVERT: A 410 MET cc_start: 0.8936 (mmm) cc_final: 0.8692 (tpp) REVERT: A 421 LEU cc_start: 0.9429 (tm) cc_final: 0.8942 (tm) REVERT: A 440 MET cc_start: 0.9039 (ppp) cc_final: 0.8684 (mmm) REVERT: A 442 MET cc_start: 0.8323 (mtt) cc_final: 0.7901 (tmm) REVERT: A 454 MET cc_start: 0.9251 (mtt) cc_final: 0.8932 (mmt) REVERT: A 458 LEU cc_start: 0.9803 (mm) cc_final: 0.9428 (mm) REVERT: A 463 CYS cc_start: 0.9483 (m) cc_final: 0.9249 (m) REVERT: A 465 VAL cc_start: 0.9607 (t) cc_final: 0.9237 (t) REVERT: A 478 PHE cc_start: 0.9643 (t80) cc_final: 0.9434 (t80) REVERT: A 483 GLN cc_start: 0.9692 (tt0) cc_final: 0.9314 (tp40) REVERT: A 494 CYS cc_start: 0.9114 (t) cc_final: 0.8845 (p) REVERT: A 497 MET cc_start: 0.9432 (ttp) cc_final: 0.8915 (ttp) REVERT: A 536 LEU cc_start: 0.9752 (mt) cc_final: 0.9541 (mt) REVERT: A 551 LEU cc_start: 0.8026 (mt) cc_final: 0.7542 (mp) REVERT: A 587 HIS cc_start: 0.8997 (p90) cc_final: 0.8259 (p-80) REVERT: A 588 GLU cc_start: 0.9505 (pt0) cc_final: 0.9023 (pp20) REVERT: A 591 GLU cc_start: 0.9052 (pp20) cc_final: 0.8758 (pm20) REVERT: B 57 ASP cc_start: 0.8941 (m-30) cc_final: 0.8524 (m-30) REVERT: B 70 CYS cc_start: 0.8414 (p) cc_final: 0.8051 (p) REVERT: B 78 MET cc_start: 0.8202 (ptp) cc_final: 0.7927 (ptp) REVERT: B 88 LEU cc_start: 0.9418 (tt) cc_final: 0.9191 (tt) REVERT: B 99 MET cc_start: 0.9311 (mtm) cc_final: 0.8779 (tpp) REVERT: B 113 GLU cc_start: 0.9541 (tt0) cc_final: 0.9149 (tm-30) REVERT: B 118 GLN cc_start: 0.9243 (tt0) cc_final: 0.8910 (tm-30) REVERT: B 123 ILE cc_start: 0.9373 (mt) cc_final: 0.9089 (mt) REVERT: B 128 GLN cc_start: 0.9107 (pt0) cc_final: 0.8444 (tm-30) REVERT: B 150 THR cc_start: 0.9385 (p) cc_final: 0.8954 (p) REVERT: B 169 PHE cc_start: 0.9099 (m-10) cc_final: 0.8816 (m-80) REVERT: B 200 LEU cc_start: 0.9654 (mm) cc_final: 0.9388 (mt) REVERT: B 204 ILE cc_start: 0.9590 (mt) cc_final: 0.9277 (tp) REVERT: B 234 LEU cc_start: 0.9008 (mm) cc_final: 0.8298 (mt) REVERT: B 246 LEU cc_start: 0.9616 (tp) cc_final: 0.9355 (tp) REVERT: B 294 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8823 (mt-10) REVERT: B 300 LYS cc_start: 0.9012 (mttt) cc_final: 0.8573 (mppt) REVERT: B 460 LEU cc_start: 0.9308 (mm) cc_final: 0.9024 (mm) REVERT: B 463 CYS cc_start: 0.9475 (m) cc_final: 0.9149 (m) REVERT: B 464 ASN cc_start: 0.9376 (m-40) cc_final: 0.8948 (m-40) REVERT: B 478 PHE cc_start: 0.9640 (t80) cc_final: 0.9338 (t80) REVERT: B 483 GLN cc_start: 0.9723 (tt0) cc_final: 0.9389 (tp40) REVERT: B 497 MET cc_start: 0.9427 (ttp) cc_final: 0.9003 (ttp) REVERT: B 518 GLU cc_start: 0.9242 (mt-10) cc_final: 0.9033 (pp20) REVERT: B 526 TYR cc_start: 0.8916 (t80) cc_final: 0.8628 (t80) REVERT: B 551 LEU cc_start: 0.9311 (mt) cc_final: 0.8974 (mp) REVERT: B 605 GLU cc_start: 0.9169 (tt0) cc_final: 0.8886 (tt0) REVERT: B 627 ASP cc_start: 0.9275 (m-30) cc_final: 0.9048 (t0) REVERT: C 35 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8870 (mp0) REVERT: C 39 LEU cc_start: 0.9582 (tp) cc_final: 0.9313 (tp) REVERT: C 42 LYS cc_start: 0.9378 (tttt) cc_final: 0.9091 (pttt) REVERT: C 83 LEU cc_start: 0.9756 (tp) cc_final: 0.9513 (tp) REVERT: C 84 HIS cc_start: 0.9110 (m90) cc_final: 0.8272 (m170) REVERT: C 93 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8942 (pm20) REVERT: C 96 MET cc_start: 0.9251 (mmt) cc_final: 0.9011 (mmm) REVERT: C 99 MET cc_start: 0.8940 (mtm) cc_final: 0.8531 (ptp) REVERT: C 113 GLU cc_start: 0.9384 (tt0) cc_final: 0.9095 (tm-30) REVERT: C 136 LEU cc_start: 0.9393 (mt) cc_final: 0.9113 (mt) REVERT: C 161 TYR cc_start: 0.9071 (t80) cc_final: 0.8737 (t80) REVERT: C 184 GLU cc_start: 0.9317 (pt0) cc_final: 0.8954 (tm-30) REVERT: C 200 LEU cc_start: 0.9572 (mm) cc_final: 0.9122 (mt) REVERT: C 204 ILE cc_start: 0.9577 (mt) cc_final: 0.9299 (mt) REVERT: C 246 LEU cc_start: 0.9702 (tp) cc_final: 0.9444 (tp) REVERT: C 260 MET cc_start: 0.9675 (tpt) cc_final: 0.9445 (mmm) REVERT: C 263 ARG cc_start: 0.9619 (mmt180) cc_final: 0.9404 (mmm-85) REVERT: C 297 ILE cc_start: 0.9416 (pp) cc_final: 0.9056 (tp) REVERT: C 300 LYS cc_start: 0.9044 (mttt) cc_final: 0.8533 (mppt) REVERT: C 303 GLU cc_start: 0.9303 (pt0) cc_final: 0.8784 (pp20) REVERT: C 306 GLN cc_start: 0.9104 (pt0) cc_final: 0.8604 (pm20) REVERT: C 327 PRO cc_start: 0.9194 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: C 343 PHE cc_start: 0.9660 (t80) cc_final: 0.9458 (t80) REVERT: C 347 CYS cc_start: 0.9155 (m) cc_final: 0.8894 (m) REVERT: C 367 LEU cc_start: 0.9613 (tt) cc_final: 0.9358 (tp) REVERT: C 403 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9095 (tp30) REVERT: C 421 LEU cc_start: 0.9443 (tm) cc_final: 0.9053 (tm) REVERT: C 463 CYS cc_start: 0.9331 (m) cc_final: 0.9088 (m) REVERT: C 478 PHE cc_start: 0.9609 (t80) cc_final: 0.9309 (t80) REVERT: C 494 CYS cc_start: 0.9113 (t) cc_final: 0.8735 (p) REVERT: C 497 MET cc_start: 0.9549 (ttp) cc_final: 0.9161 (tmm) REVERT: C 536 LEU cc_start: 0.9754 (mt) cc_final: 0.9543 (mt) REVERT: C 538 LEU cc_start: 0.9640 (mp) cc_final: 0.9434 (mp) REVERT: C 541 ILE cc_start: 0.9303 (pt) cc_final: 0.9081 (pt) REVERT: C 577 MET cc_start: 0.9199 (ptm) cc_final: 0.8562 (ppp) REVERT: D 35 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8872 (mt-10) REVERT: D 49 LEU cc_start: 0.9402 (pt) cc_final: 0.9093 (mp) REVERT: D 84 HIS cc_start: 0.9157 (m90) cc_final: 0.8407 (m-70) REVERT: D 93 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9029 (pm20) REVERT: D 99 MET cc_start: 0.9032 (mtm) cc_final: 0.8738 (ptp) REVERT: D 113 GLU cc_start: 0.9413 (tt0) cc_final: 0.9024 (tm-30) REVERT: D 122 HIS cc_start: 0.9522 (m170) cc_final: 0.9298 (m-70) REVERT: D 136 LEU cc_start: 0.9457 (mt) cc_final: 0.9166 (mt) REVERT: D 161 TYR cc_start: 0.8891 (t80) cc_final: 0.8616 (t80) REVERT: D 200 LEU cc_start: 0.9518 (mm) cc_final: 0.9023 (mt) REVERT: D 204 ILE cc_start: 0.9573 (mt) cc_final: 0.9262 (mt) REVERT: D 209 LYS cc_start: 0.8623 (mttt) cc_final: 0.7822 (mttt) REVERT: D 246 LEU cc_start: 0.9690 (tp) cc_final: 0.9407 (tp) REVERT: D 250 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8404 (mm-30) REVERT: D 259 LEU cc_start: 0.9480 (mm) cc_final: 0.9120 (mm) REVERT: D 260 MET cc_start: 0.9635 (tpt) cc_final: 0.9392 (mmm) REVERT: D 300 LYS cc_start: 0.8877 (mttt) cc_final: 0.8387 (mppt) REVERT: D 306 GLN cc_start: 0.9139 (pt0) cc_final: 0.8473 (mp10) REVERT: D 336 TYR cc_start: 0.9183 (t80) cc_final: 0.8861 (t80) REVERT: D 343 PHE cc_start: 0.9745 (t80) cc_final: 0.9411 (t80) REVERT: D 347 CYS cc_start: 0.9335 (m) cc_final: 0.8900 (m) REVERT: D 367 LEU cc_start: 0.9621 (tt) cc_final: 0.9269 (tt) REVERT: D 403 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8851 (tp30) REVERT: D 410 MET cc_start: 0.9048 (mmm) cc_final: 0.8798 (tmm) REVERT: D 418 GLN cc_start: 0.9518 (tp40) cc_final: 0.9291 (mp10) REVERT: D 463 CYS cc_start: 0.9384 (m) cc_final: 0.9104 (m) REVERT: D 478 PHE cc_start: 0.9586 (t80) cc_final: 0.9328 (t80) REVERT: D 483 GLN cc_start: 0.9704 (tt0) cc_final: 0.9426 (mm-40) REVERT: D 494 CYS cc_start: 0.9167 (t) cc_final: 0.8779 (p) REVERT: D 536 LEU cc_start: 0.9772 (mt) cc_final: 0.9533 (mt) REVERT: D 537 PHE cc_start: 0.9435 (t80) cc_final: 0.9231 (t80) REVERT: D 538 LEU cc_start: 0.9601 (mp) cc_final: 0.9400 (mp) REVERT: D 541 ILE cc_start: 0.9197 (pt) cc_final: 0.8869 (pt) REVERT: D 577 MET cc_start: 0.9243 (ptm) cc_final: 0.8618 (ppp) outliers start: 12 outliers final: 8 residues processed: 1065 average time/residue: 0.3152 time to fit residues: 521.3530 Evaluate side-chains 740 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 732 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 75 optimal weight: 0.0470 chunk 118 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 91 ASN A 118 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 267 GLN A 572 ASN A 582 HIS A 596 GLN B 74 GLN B 91 ASN B 118 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 582 HIS B 596 GLN C 91 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 572 ASN C 582 HIS C 596 GLN C 637 GLN D 74 GLN D 91 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN D 596 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20602 Z= 0.183 Angle : 0.738 10.388 27945 Z= 0.370 Chirality : 0.045 0.199 3138 Planarity : 0.006 0.066 3522 Dihedral : 10.206 102.385 2798 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.15), residues: 2472 helix: -1.65 (0.13), residues: 1284 sheet: -3.74 (0.59), residues: 48 loop : -2.78 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 593 HIS 0.011 0.001 HIS B 522 PHE 0.016 0.001 PHE C 537 TYR 0.015 0.001 TYR C 547 ARG 0.014 0.001 ARG B 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 933 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 113 GLU cc_start: 0.9347 (tt0) cc_final: 0.8945 (tm-30) REVERT: A 122 HIS cc_start: 0.9546 (m170) cc_final: 0.9253 (m170) REVERT: A 146 ARG cc_start: 0.9380 (mtt180) cc_final: 0.8911 (mmm-85) REVERT: A 169 PHE cc_start: 0.9381 (m-80) cc_final: 0.8517 (m-80) REVERT: A 198 THR cc_start: 0.9676 (t) cc_final: 0.9052 (t) REVERT: A 201 HIS cc_start: 0.9339 (m-70) cc_final: 0.8901 (m90) REVERT: A 215 MET cc_start: 0.9496 (mmm) cc_final: 0.9160 (mmm) REVERT: A 245 LYS cc_start: 0.8481 (mttt) cc_final: 0.8163 (mtpt) REVERT: A 250 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8411 (tp30) REVERT: A 255 MET cc_start: 0.9354 (mmp) cc_final: 0.8798 (tpp) REVERT: A 300 LYS cc_start: 0.8977 (mttt) cc_final: 0.8528 (mppt) REVERT: A 301 LYS cc_start: 0.9312 (tptp) cc_final: 0.8977 (tmtt) REVERT: A 303 GLU cc_start: 0.9411 (tt0) cc_final: 0.9195 (tp30) REVERT: A 306 GLN cc_start: 0.8972 (pt0) cc_final: 0.8400 (mp10) REVERT: A 343 PHE cc_start: 0.9535 (t80) cc_final: 0.9330 (t80) REVERT: A 382 ASP cc_start: 0.7683 (m-30) cc_final: 0.7149 (m-30) REVERT: A 401 LEU cc_start: 0.9285 (mt) cc_final: 0.9084 (mt) REVERT: A 403 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8863 (tp30) REVERT: A 421 LEU cc_start: 0.9123 (tt) cc_final: 0.8880 (tt) REVERT: A 437 LEU cc_start: 0.9652 (mm) cc_final: 0.9366 (mp) REVERT: A 454 MET cc_start: 0.9209 (mtt) cc_final: 0.8745 (mmt) REVERT: A 463 CYS cc_start: 0.9289 (m) cc_final: 0.9050 (m) REVERT: A 466 MET cc_start: 0.9718 (mtt) cc_final: 0.9428 (mmm) REVERT: A 483 GLN cc_start: 0.9709 (tt0) cc_final: 0.9328 (tp40) REVERT: A 491 MET cc_start: 0.8742 (ttt) cc_final: 0.8526 (ttt) REVERT: A 494 CYS cc_start: 0.9196 (t) cc_final: 0.8936 (p) REVERT: A 497 MET cc_start: 0.9428 (ttp) cc_final: 0.8774 (ttp) REVERT: A 534 PHE cc_start: 0.9022 (t80) cc_final: 0.8792 (t80) REVERT: A 536 LEU cc_start: 0.9718 (mt) cc_final: 0.9517 (mt) REVERT: A 537 PHE cc_start: 0.9572 (t80) cc_final: 0.8418 (t80) REVERT: A 538 LEU cc_start: 0.9463 (mp) cc_final: 0.8986 (mp) REVERT: A 551 LEU cc_start: 0.7921 (mt) cc_final: 0.7576 (mp) REVERT: A 569 LEU cc_start: 0.9812 (tp) cc_final: 0.9567 (tp) REVERT: A 580 ASP cc_start: 0.8327 (m-30) cc_final: 0.7816 (m-30) REVERT: A 588 GLU cc_start: 0.9351 (pt0) cc_final: 0.8988 (pp20) REVERT: A 590 ASP cc_start: 0.8881 (p0) cc_final: 0.8673 (p0) REVERT: A 605 GLU cc_start: 0.9217 (tt0) cc_final: 0.8989 (tt0) REVERT: B 70 CYS cc_start: 0.8435 (p) cc_final: 0.7667 (p) REVERT: B 93 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8869 (pm20) REVERT: B 99 MET cc_start: 0.9272 (mtm) cc_final: 0.8866 (ptp) REVERT: B 113 GLU cc_start: 0.9528 (tt0) cc_final: 0.9053 (tm-30) REVERT: B 118 GLN cc_start: 0.9402 (tt0) cc_final: 0.9064 (tp40) REVERT: B 122 HIS cc_start: 0.9586 (m170) cc_final: 0.9187 (m-70) REVERT: B 128 GLN cc_start: 0.9147 (pt0) cc_final: 0.8406 (tm-30) REVERT: B 131 ASN cc_start: 0.9584 (m110) cc_final: 0.9352 (t0) REVERT: B 174 ASN cc_start: 0.8847 (t0) cc_final: 0.8585 (p0) REVERT: B 209 LYS cc_start: 0.9333 (mttt) cc_final: 0.8763 (ttmt) REVERT: B 219 LEU cc_start: 0.9783 (mt) cc_final: 0.9482 (mm) REVERT: B 245 LYS cc_start: 0.9238 (mttt) cc_final: 0.8799 (ptpp) REVERT: B 255 MET cc_start: 0.9060 (tpt) cc_final: 0.8782 (tpp) REVERT: B 259 LEU cc_start: 0.9689 (mm) cc_final: 0.9376 (mm) REVERT: B 260 MET cc_start: 0.9613 (mmm) cc_final: 0.9179 (mmm) REVERT: B 294 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8738 (mt-10) REVERT: B 297 ILE cc_start: 0.9503 (pt) cc_final: 0.9088 (tp) REVERT: B 300 LYS cc_start: 0.8932 (mttt) cc_final: 0.8520 (mppt) REVERT: B 306 GLN cc_start: 0.8810 (pt0) cc_final: 0.8407 (mp10) REVERT: B 403 GLU cc_start: 0.8924 (tp30) cc_final: 0.8709 (tp30) REVERT: B 421 LEU cc_start: 0.9248 (tt) cc_final: 0.8599 (tt) REVERT: B 454 MET cc_start: 0.9465 (mmt) cc_final: 0.8846 (tpp) REVERT: B 463 CYS cc_start: 0.9338 (m) cc_final: 0.9079 (m) REVERT: B 483 GLN cc_start: 0.9743 (tt0) cc_final: 0.9394 (mm-40) REVERT: B 491 MET cc_start: 0.8534 (ttt) cc_final: 0.8286 (ttt) REVERT: B 494 CYS cc_start: 0.8938 (t) cc_final: 0.8691 (p) REVERT: B 497 MET cc_start: 0.9239 (ttp) cc_final: 0.8572 (ttp) REVERT: B 526 TYR cc_start: 0.8926 (t80) cc_final: 0.8706 (t80) REVERT: B 528 MET cc_start: 0.8358 (mmp) cc_final: 0.8021 (tpp) REVERT: B 537 PHE cc_start: 0.9373 (t80) cc_final: 0.8308 (t80) REVERT: B 538 LEU cc_start: 0.9275 (mp) cc_final: 0.8807 (mp) REVERT: B 554 MET cc_start: 0.8936 (tpt) cc_final: 0.8623 (tpt) REVERT: B 568 LEU cc_start: 0.9571 (tp) cc_final: 0.9343 (tp) REVERT: B 603 MET cc_start: 0.9658 (ttp) cc_final: 0.9101 (tmm) REVERT: B 604 LEU cc_start: 0.9817 (mm) cc_final: 0.9315 (mm) REVERT: B 605 GLU cc_start: 0.8981 (tt0) cc_final: 0.8780 (tt0) REVERT: C 35 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8905 (mp0) REVERT: C 50 LEU cc_start: 0.9588 (mp) cc_final: 0.8803 (tt) REVERT: C 93 GLU cc_start: 0.9338 (mt-10) cc_final: 0.8980 (pm20) REVERT: C 96 MET cc_start: 0.9235 (mmt) cc_final: 0.8896 (mmm) REVERT: C 99 MET cc_start: 0.8887 (mtm) cc_final: 0.8459 (ptp) REVERT: C 113 GLU cc_start: 0.9409 (tt0) cc_final: 0.9147 (tm-30) REVERT: C 131 ASN cc_start: 0.9480 (m110) cc_final: 0.9250 (p0) REVERT: C 198 THR cc_start: 0.9626 (t) cc_final: 0.9396 (m) REVERT: C 204 ILE cc_start: 0.9519 (mt) cc_final: 0.9228 (mt) REVERT: C 209 LYS cc_start: 0.8829 (mttt) cc_final: 0.8201 (ttmt) REVERT: C 215 MET cc_start: 0.9380 (mmp) cc_final: 0.9099 (mmm) REVERT: C 245 LYS cc_start: 0.9013 (mttt) cc_final: 0.8385 (ptpp) REVERT: C 255 MET cc_start: 0.9058 (tpt) cc_final: 0.8721 (tpp) REVERT: C 259 LEU cc_start: 0.9603 (mm) cc_final: 0.9317 (mm) REVERT: C 300 LYS cc_start: 0.8955 (mttt) cc_final: 0.8467 (mppt) REVERT: C 301 LYS cc_start: 0.8818 (tttt) cc_final: 0.8334 (ttpt) REVERT: C 303 GLU cc_start: 0.9214 (pt0) cc_final: 0.8892 (pp20) REVERT: C 306 GLN cc_start: 0.8984 (pt0) cc_final: 0.8709 (pm20) REVERT: C 343 PHE cc_start: 0.9499 (t80) cc_final: 0.9249 (t80) REVERT: C 347 CYS cc_start: 0.8771 (m) cc_final: 0.8536 (m) REVERT: C 403 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8965 (tp30) REVERT: C 421 LEU cc_start: 0.9115 (tt) cc_final: 0.8850 (tt) REVERT: C 440 MET cc_start: 0.8622 (mmm) cc_final: 0.8251 (mmp) REVERT: C 463 CYS cc_start: 0.9210 (m) cc_final: 0.8826 (m) REVERT: C 483 GLN cc_start: 0.9735 (tt0) cc_final: 0.9341 (tp40) REVERT: C 494 CYS cc_start: 0.9059 (t) cc_final: 0.8770 (p) REVERT: C 497 MET cc_start: 0.9326 (ttp) cc_final: 0.8941 (tmm) REVERT: C 537 PHE cc_start: 0.9441 (t80) cc_final: 0.9229 (t80) REVERT: C 538 LEU cc_start: 0.9506 (mp) cc_final: 0.9124 (mp) REVERT: C 569 LEU cc_start: 0.9813 (tp) cc_final: 0.9595 (tp) REVERT: D 35 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8829 (mt-10) REVERT: D 39 LEU cc_start: 0.9514 (tp) cc_final: 0.9215 (tp) REVERT: D 42 LYS cc_start: 0.9214 (tttt) cc_final: 0.9007 (pttt) REVERT: D 84 HIS cc_start: 0.9047 (m90) cc_final: 0.8522 (m90) REVERT: D 93 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9000 (pm20) REVERT: D 96 MET cc_start: 0.9194 (mmp) cc_final: 0.8860 (mmm) REVERT: D 99 MET cc_start: 0.8992 (mtm) cc_final: 0.8664 (ptp) REVERT: D 113 GLU cc_start: 0.9562 (tt0) cc_final: 0.9135 (tm-30) REVERT: D 136 LEU cc_start: 0.9432 (mt) cc_final: 0.8997 (mt) REVERT: D 159 LEU cc_start: 0.8690 (mm) cc_final: 0.8447 (mm) REVERT: D 204 ILE cc_start: 0.9499 (mt) cc_final: 0.9206 (mt) REVERT: D 209 LYS cc_start: 0.8663 (mttt) cc_final: 0.8322 (mtpt) REVERT: D 215 MET cc_start: 0.9451 (mmp) cc_final: 0.9195 (mmm) REVERT: D 245 LYS cc_start: 0.8848 (mttt) cc_final: 0.8148 (ptpp) REVERT: D 246 LEU cc_start: 0.9685 (tp) cc_final: 0.9467 (tp) REVERT: D 250 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8459 (mm-30) REVERT: D 255 MET cc_start: 0.9290 (mmp) cc_final: 0.8934 (tpp) REVERT: D 259 LEU cc_start: 0.9502 (mm) cc_final: 0.9093 (mm) REVERT: D 260 MET cc_start: 0.9620 (tpt) cc_final: 0.9413 (mmm) REVERT: D 300 LYS cc_start: 0.8878 (mttt) cc_final: 0.8382 (mppt) REVERT: D 301 LYS cc_start: 0.9520 (tptp) cc_final: 0.9265 (tmtt) REVERT: D 343 PHE cc_start: 0.9447 (t80) cc_final: 0.9148 (t80) REVERT: D 347 CYS cc_start: 0.8851 (m) cc_final: 0.8470 (m) REVERT: D 403 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8873 (tp30) REVERT: D 437 LEU cc_start: 0.9435 (mm) cc_final: 0.9190 (mp) REVERT: D 440 MET cc_start: 0.8179 (mmm) cc_final: 0.7796 (mmm) REVERT: D 463 CYS cc_start: 0.9292 (m) cc_final: 0.9084 (m) REVERT: D 483 GLN cc_start: 0.9736 (tt0) cc_final: 0.9404 (mm-40) REVERT: D 494 CYS cc_start: 0.9145 (t) cc_final: 0.8849 (p) REVERT: D 536 LEU cc_start: 0.9772 (mt) cc_final: 0.9549 (mt) REVERT: D 537 PHE cc_start: 0.9624 (t80) cc_final: 0.9319 (t80) REVERT: D 538 LEU cc_start: 0.9523 (mp) cc_final: 0.8781 (mp) REVERT: D 569 LEU cc_start: 0.9776 (tp) cc_final: 0.9500 (tp) REVERT: D 593 TRP cc_start: 0.9218 (t60) cc_final: 0.8934 (t60) REVERT: D 629 TRP cc_start: 0.8769 (m100) cc_final: 0.8428 (m-10) outliers start: 2 outliers final: 0 residues processed: 933 average time/residue: 0.2799 time to fit residues: 411.7168 Evaluate side-chains 715 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 715 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 153 optimal weight: 0.0030 chunk 62 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 201 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 201 HIS B 265 HIS B 522 HIS ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 572 ASN D 37 ASN D 74 GLN D 201 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20602 Z= 0.247 Angle : 0.730 7.839 27945 Z= 0.371 Chirality : 0.045 0.176 3138 Planarity : 0.005 0.063 3522 Dihedral : 9.757 104.649 2798 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2472 helix: -0.74 (0.14), residues: 1288 sheet: -3.68 (0.60), residues: 48 loop : -2.60 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 593 HIS 0.009 0.001 HIS D 84 PHE 0.018 0.002 PHE B 468 TYR 0.018 0.002 TYR C 547 ARG 0.004 0.000 ARG C 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 876 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 39 LEU cc_start: 0.9516 (tp) cc_final: 0.9044 (tp) REVERT: A 42 LYS cc_start: 0.9429 (tttt) cc_final: 0.9097 (pptt) REVERT: A 84 HIS cc_start: 0.9157 (m90) cc_final: 0.8914 (m170) REVERT: A 113 GLU cc_start: 0.9380 (tt0) cc_final: 0.8991 (tm-30) REVERT: A 146 ARG cc_start: 0.9435 (mtt180) cc_final: 0.8954 (mmm-85) REVERT: A 215 MET cc_start: 0.9532 (mmm) cc_final: 0.9171 (mmm) REVERT: A 245 LYS cc_start: 0.8660 (mttt) cc_final: 0.8325 (mttm) REVERT: A 260 MET cc_start: 0.9619 (tpt) cc_final: 0.9321 (mmm) REVERT: A 297 ILE cc_start: 0.9520 (mm) cc_final: 0.9179 (tp) REVERT: A 300 LYS cc_start: 0.9082 (mttt) cc_final: 0.8544 (mppt) REVERT: A 301 LYS cc_start: 0.9316 (tptp) cc_final: 0.9018 (tmtt) REVERT: A 303 GLU cc_start: 0.9457 (tt0) cc_final: 0.9154 (tp30) REVERT: A 306 GLN cc_start: 0.9053 (pt0) cc_final: 0.8733 (pt0) REVERT: A 343 PHE cc_start: 0.9590 (t80) cc_final: 0.9383 (t80) REVERT: A 403 GLU cc_start: 0.9321 (mm-30) cc_final: 0.8971 (tp30) REVERT: A 410 MET cc_start: 0.9262 (tpt) cc_final: 0.8652 (tpp) REVERT: A 440 MET cc_start: 0.7909 (mmm) cc_final: 0.7508 (mmm) REVERT: A 454 MET cc_start: 0.9272 (mtt) cc_final: 0.8917 (mmt) REVERT: A 466 MET cc_start: 0.9733 (mtt) cc_final: 0.9522 (mtt) REVERT: A 483 GLN cc_start: 0.9743 (tt0) cc_final: 0.9391 (tp40) REVERT: A 491 MET cc_start: 0.8871 (ttt) cc_final: 0.8645 (ttt) REVERT: A 497 MET cc_start: 0.9461 (ttp) cc_final: 0.8759 (ttp) REVERT: A 518 GLU cc_start: 0.9099 (mp0) cc_final: 0.8896 (mp0) REVERT: A 537 PHE cc_start: 0.9585 (t80) cc_final: 0.8477 (t80) REVERT: A 538 LEU cc_start: 0.9338 (mp) cc_final: 0.9089 (mp) REVERT: A 541 ILE cc_start: 0.8688 (pt) cc_final: 0.8486 (mm) REVERT: A 551 LEU cc_start: 0.8090 (mt) cc_final: 0.7816 (mp) REVERT: A 570 MET cc_start: 0.9305 (mmp) cc_final: 0.8935 (mmm) REVERT: A 577 MET cc_start: 0.9240 (mmp) cc_final: 0.8944 (mmm) REVERT: B 35 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8812 (mt-10) REVERT: B 57 ASP cc_start: 0.9143 (m-30) cc_final: 0.8846 (m-30) REVERT: B 93 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8926 (pm20) REVERT: B 96 MET cc_start: 0.9585 (mmt) cc_final: 0.9274 (mmp) REVERT: B 98 LEU cc_start: 0.9670 (mt) cc_final: 0.9416 (pp) REVERT: B 99 MET cc_start: 0.9404 (mtm) cc_final: 0.9014 (mtm) REVERT: B 110 MET cc_start: 0.9024 (mmm) cc_final: 0.8812 (mmm) REVERT: B 113 GLU cc_start: 0.9510 (tt0) cc_final: 0.9116 (tm-30) REVERT: B 118 GLN cc_start: 0.9555 (tt0) cc_final: 0.9117 (tm-30) REVERT: B 123 ILE cc_start: 0.9636 (mt) cc_final: 0.9387 (mt) REVERT: B 128 GLN cc_start: 0.9145 (pt0) cc_final: 0.8401 (tm-30) REVERT: B 174 ASN cc_start: 0.8943 (t0) cc_final: 0.8596 (t0) REVERT: B 182 LEU cc_start: 0.9801 (mm) cc_final: 0.9541 (mm) REVERT: B 195 LEU cc_start: 0.9590 (mm) cc_final: 0.9378 (mp) REVERT: B 204 ILE cc_start: 0.9422 (mt) cc_final: 0.9138 (tp) REVERT: B 209 LYS cc_start: 0.9266 (mttt) cc_final: 0.8721 (ttmt) REVERT: B 246 LEU cc_start: 0.9597 (tp) cc_final: 0.9376 (tp) REVERT: B 260 MET cc_start: 0.9614 (mmm) cc_final: 0.9183 (mmm) REVERT: B 294 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 300 LYS cc_start: 0.8964 (mttt) cc_final: 0.8467 (mppt) REVERT: B 303 GLU cc_start: 0.9040 (tp30) cc_final: 0.8419 (tp30) REVERT: B 306 GLN cc_start: 0.8881 (pt0) cc_final: 0.8416 (pm20) REVERT: B 403 GLU cc_start: 0.9019 (tp30) cc_final: 0.8777 (tp30) REVERT: B 410 MET cc_start: 0.9192 (tmm) cc_final: 0.8876 (tmm) REVERT: B 454 MET cc_start: 0.9541 (mmt) cc_final: 0.8921 (tpp) REVERT: B 463 CYS cc_start: 0.9297 (m) cc_final: 0.8975 (m) REVERT: B 483 GLN cc_start: 0.9729 (tt0) cc_final: 0.9261 (tp40) REVERT: B 491 MET cc_start: 0.8648 (ttt) cc_final: 0.8408 (ttt) REVERT: B 494 CYS cc_start: 0.8974 (t) cc_final: 0.8739 (p) REVERT: B 497 MET cc_start: 0.9273 (ttp) cc_final: 0.8699 (ttp) REVERT: B 528 MET cc_start: 0.8330 (mmp) cc_final: 0.8016 (tpp) REVERT: B 537 PHE cc_start: 0.9454 (t80) cc_final: 0.8241 (t80) REVERT: B 538 LEU cc_start: 0.9272 (mp) cc_final: 0.8777 (mp) REVERT: B 541 ILE cc_start: 0.8838 (pt) cc_final: 0.8499 (pt) REVERT: B 554 MET cc_start: 0.8877 (tpt) cc_final: 0.8630 (tpt) REVERT: B 569 LEU cc_start: 0.9799 (tp) cc_final: 0.9587 (tp) REVERT: B 570 MET cc_start: 0.9335 (mmm) cc_final: 0.9085 (mmm) REVERT: B 574 LEU cc_start: 0.9930 (tp) cc_final: 0.9521 (tp) REVERT: B 605 GLU cc_start: 0.9044 (tt0) cc_final: 0.8584 (tt0) REVERT: C 34 ASP cc_start: 0.9570 (m-30) cc_final: 0.9276 (m-30) REVERT: C 35 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8880 (mt-10) REVERT: C 84 HIS cc_start: 0.9038 (m90) cc_final: 0.8618 (m90) REVERT: C 93 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9025 (pm20) REVERT: C 96 MET cc_start: 0.9324 (mmt) cc_final: 0.8957 (mmm) REVERT: C 204 ILE cc_start: 0.9585 (mt) cc_final: 0.9265 (mt) REVERT: C 209 LYS cc_start: 0.8919 (mttt) cc_final: 0.8287 (ttmt) REVERT: C 215 MET cc_start: 0.9402 (mmp) cc_final: 0.9126 (mmm) REVERT: C 245 LYS cc_start: 0.9095 (mttt) cc_final: 0.8520 (ptpp) REVERT: C 246 LEU cc_start: 0.9665 (tp) cc_final: 0.9439 (tp) REVERT: C 250 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8572 (mm-30) REVERT: C 255 MET cc_start: 0.9197 (tpt) cc_final: 0.8923 (tpp) REVERT: C 259 LEU cc_start: 0.9661 (mm) cc_final: 0.9455 (mm) REVERT: C 260 MET cc_start: 0.9415 (mmp) cc_final: 0.8981 (mmm) REVERT: C 294 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8490 (mt-10) REVERT: C 297 ILE cc_start: 0.9503 (mm) cc_final: 0.9282 (tp) REVERT: C 300 LYS cc_start: 0.9114 (mttt) cc_final: 0.8658 (mppt) REVERT: C 306 GLN cc_start: 0.9055 (pt0) cc_final: 0.8741 (pm20) REVERT: C 343 PHE cc_start: 0.9606 (t80) cc_final: 0.9369 (t80) REVERT: C 403 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8978 (tp30) REVERT: C 410 MET cc_start: 0.9357 (tmm) cc_final: 0.9030 (tmm) REVERT: C 454 MET cc_start: 0.9528 (tpp) cc_final: 0.9156 (tpp) REVERT: C 483 GLN cc_start: 0.9746 (tt0) cc_final: 0.9417 (tt0) REVERT: C 485 MET cc_start: 0.9697 (mtp) cc_final: 0.9490 (mmm) REVERT: C 497 MET cc_start: 0.9361 (ttp) cc_final: 0.8773 (tmm) REVERT: C 538 LEU cc_start: 0.9323 (mp) cc_final: 0.8958 (mp) REVERT: C 570 MET cc_start: 0.9238 (mmp) cc_final: 0.8988 (mmm) REVERT: C 593 TRP cc_start: 0.9289 (t60) cc_final: 0.8901 (t60) REVERT: D 35 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8877 (mt-10) REVERT: D 39 LEU cc_start: 0.9525 (tp) cc_final: 0.9265 (tp) REVERT: D 42 LYS cc_start: 0.9245 (tttt) cc_final: 0.9011 (pttt) REVERT: D 50 LEU cc_start: 0.9621 (mp) cc_final: 0.9396 (mp) REVERT: D 93 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9026 (pm20) REVERT: D 96 MET cc_start: 0.9331 (mmp) cc_final: 0.8889 (mmm) REVERT: D 99 MET cc_start: 0.9032 (mtm) cc_final: 0.8642 (ptp) REVERT: D 113 GLU cc_start: 0.9563 (tt0) cc_final: 0.9273 (tm-30) REVERT: D 136 LEU cc_start: 0.9465 (mt) cc_final: 0.9161 (mt) REVERT: D 204 ILE cc_start: 0.9569 (mt) cc_final: 0.9262 (mt) REVERT: D 209 LYS cc_start: 0.8693 (mttt) cc_final: 0.8176 (ttmt) REVERT: D 215 MET cc_start: 0.9459 (mmp) cc_final: 0.9134 (mmm) REVERT: D 245 LYS cc_start: 0.8951 (mttt) cc_final: 0.8252 (ptpp) REVERT: D 246 LEU cc_start: 0.9712 (tp) cc_final: 0.9476 (tp) REVERT: D 250 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8568 (mm-30) REVERT: D 260 MET cc_start: 0.9667 (tpt) cc_final: 0.9444 (mmm) REVERT: D 300 LYS cc_start: 0.8996 (mttt) cc_final: 0.8511 (mppt) REVERT: D 301 LYS cc_start: 0.9476 (tptp) cc_final: 0.9185 (tmtt) REVERT: D 303 GLU cc_start: 0.9203 (tp30) cc_final: 0.8884 (tp30) REVERT: D 403 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8960 (tp30) REVERT: D 410 MET cc_start: 0.9299 (tpt) cc_final: 0.8624 (tpp) REVERT: D 440 MET cc_start: 0.8273 (mmm) cc_final: 0.7820 (mmm) REVERT: D 463 CYS cc_start: 0.9308 (m) cc_final: 0.9074 (m) REVERT: D 483 GLN cc_start: 0.9760 (tt0) cc_final: 0.9434 (tp40) REVERT: D 494 CYS cc_start: 0.9143 (t) cc_final: 0.8801 (p) REVERT: D 536 LEU cc_start: 0.9763 (mt) cc_final: 0.9557 (mt) REVERT: D 570 MET cc_start: 0.9249 (mmp) cc_final: 0.8914 (mmm) REVERT: D 574 LEU cc_start: 0.9762 (tp) cc_final: 0.9513 (tp) REVERT: D 577 MET cc_start: 0.8911 (ppp) cc_final: 0.8679 (ppp) REVERT: D 593 TRP cc_start: 0.9322 (t60) cc_final: 0.8613 (t60) outliers start: 1 outliers final: 0 residues processed: 876 average time/residue: 0.2691 time to fit residues: 375.5646 Evaluate side-chains 700 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 0.0770 chunk 169 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 151 optimal weight: 0.0070 chunk 226 optimal weight: 0.0970 chunk 239 optimal weight: 0.0470 chunk 118 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.1652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20602 Z= 0.166 Angle : 0.695 8.183 27945 Z= 0.335 Chirality : 0.044 0.161 3138 Planarity : 0.004 0.063 3522 Dihedral : 8.640 103.337 2798 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2472 helix: -0.66 (0.14), residues: 1404 sheet: -3.77 (0.60), residues: 48 loop : -2.82 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 629 HIS 0.009 0.001 HIS C 84 PHE 0.029 0.001 PHE A 508 TYR 0.013 0.001 TYR D 161 ARG 0.006 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 862 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8767 (mt-10) REVERT: A 84 HIS cc_start: 0.9071 (m90) cc_final: 0.8740 (m170) REVERT: A 113 GLU cc_start: 0.9371 (tt0) cc_final: 0.8948 (tm-30) REVERT: A 122 HIS cc_start: 0.9470 (m170) cc_final: 0.8976 (m-70) REVERT: A 123 ILE cc_start: 0.9659 (mm) cc_final: 0.9385 (tt) REVERT: A 146 ARG cc_start: 0.9423 (mtt180) cc_final: 0.8955 (mmm-85) REVERT: A 169 PHE cc_start: 0.9279 (m-80) cc_final: 0.8539 (m-80) REVERT: A 178 ILE cc_start: 0.9640 (mp) cc_final: 0.9434 (mp) REVERT: A 198 THR cc_start: 0.9666 (t) cc_final: 0.9085 (m) REVERT: A 201 HIS cc_start: 0.9424 (m90) cc_final: 0.8995 (m90) REVERT: A 215 MET cc_start: 0.9496 (mmm) cc_final: 0.9156 (mmm) REVERT: A 245 LYS cc_start: 0.8548 (mttt) cc_final: 0.8154 (mtpp) REVERT: A 246 LEU cc_start: 0.9707 (tp) cc_final: 0.9499 (tp) REVERT: A 250 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8562 (mm-30) REVERT: A 255 MET cc_start: 0.9348 (mmm) cc_final: 0.8694 (tpp) REVERT: A 260 MET cc_start: 0.9607 (tpt) cc_final: 0.9297 (mmm) REVERT: A 297 ILE cc_start: 0.9486 (mm) cc_final: 0.9114 (tp) REVERT: A 300 LYS cc_start: 0.9111 (mttt) cc_final: 0.8578 (mppt) REVERT: A 301 LYS cc_start: 0.9296 (tptp) cc_final: 0.9068 (tptp) REVERT: A 306 GLN cc_start: 0.9015 (pt0) cc_final: 0.8733 (pm20) REVERT: A 403 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8874 (tp30) REVERT: A 410 MET cc_start: 0.9203 (tpt) cc_final: 0.8565 (tpp) REVERT: A 440 MET cc_start: 0.7934 (mmm) cc_final: 0.7524 (mmm) REVERT: A 454 MET cc_start: 0.9140 (mtt) cc_final: 0.8805 (mmt) REVERT: A 463 CYS cc_start: 0.9422 (m) cc_final: 0.9194 (m) REVERT: A 483 GLN cc_start: 0.9700 (tt0) cc_final: 0.9362 (tt0) REVERT: A 497 MET cc_start: 0.9316 (ttp) cc_final: 0.8774 (ttp) REVERT: A 537 PHE cc_start: 0.9586 (t80) cc_final: 0.8419 (t80) REVERT: A 538 LEU cc_start: 0.9233 (mp) cc_final: 0.8950 (mp) REVERT: A 551 LEU cc_start: 0.8090 (mt) cc_final: 0.7833 (mp) REVERT: A 570 MET cc_start: 0.9298 (mmp) cc_final: 0.8976 (mmm) REVERT: A 605 GLU cc_start: 0.9261 (tt0) cc_final: 0.9013 (tt0) REVERT: B 57 ASP cc_start: 0.9200 (m-30) cc_final: 0.8931 (m-30) REVERT: B 70 CYS cc_start: 0.8599 (p) cc_final: 0.8137 (p) REVERT: B 83 LEU cc_start: 0.9861 (tp) cc_final: 0.9614 (mt) REVERT: B 93 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8868 (pm20) REVERT: B 96 MET cc_start: 0.9570 (mmt) cc_final: 0.9304 (mmm) REVERT: B 105 LEU cc_start: 0.9576 (tp) cc_final: 0.9109 (tp) REVERT: B 113 GLU cc_start: 0.9502 (tt0) cc_final: 0.9086 (tm-30) REVERT: B 118 GLN cc_start: 0.9587 (tt0) cc_final: 0.9140 (tm-30) REVERT: B 123 ILE cc_start: 0.9615 (mt) cc_final: 0.9334 (mt) REVERT: B 128 GLN cc_start: 0.9018 (pt0) cc_final: 0.8140 (tm-30) REVERT: B 204 ILE cc_start: 0.9457 (mt) cc_final: 0.9181 (tp) REVERT: B 209 LYS cc_start: 0.9232 (mttt) cc_final: 0.8678 (ttmt) REVERT: B 245 LYS cc_start: 0.9402 (mttt) cc_final: 0.8897 (ptpp) REVERT: B 246 LEU cc_start: 0.9603 (tp) cc_final: 0.9363 (tp) REVERT: B 255 MET cc_start: 0.9317 (tpp) cc_final: 0.9031 (tpp) REVERT: B 259 LEU cc_start: 0.9730 (mm) cc_final: 0.9507 (mm) REVERT: B 260 MET cc_start: 0.9603 (mmm) cc_final: 0.9139 (mmm) REVERT: B 294 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 297 ILE cc_start: 0.9465 (pt) cc_final: 0.9202 (tp) REVERT: B 300 LYS cc_start: 0.8985 (mttt) cc_final: 0.8466 (mppt) REVERT: B 303 GLU cc_start: 0.8942 (tp30) cc_final: 0.8241 (tp30) REVERT: B 306 GLN cc_start: 0.8768 (pt0) cc_final: 0.8344 (pm20) REVERT: B 373 LEU cc_start: 0.9096 (mt) cc_final: 0.8892 (mt) REVERT: B 403 GLU cc_start: 0.9061 (tp30) cc_final: 0.8702 (tp30) REVERT: B 410 MET cc_start: 0.9182 (tmm) cc_final: 0.8524 (tmm) REVERT: B 421 LEU cc_start: 0.9186 (tt) cc_final: 0.8782 (tt) REVERT: B 454 MET cc_start: 0.9385 (mmt) cc_final: 0.8771 (tpp) REVERT: B 463 CYS cc_start: 0.9330 (m) cc_final: 0.9059 (m) REVERT: B 483 GLN cc_start: 0.9718 (tt0) cc_final: 0.9351 (tp40) REVERT: B 494 CYS cc_start: 0.8894 (t) cc_final: 0.8678 (p) REVERT: B 497 MET cc_start: 0.9307 (ttp) cc_final: 0.8667 (ttp) REVERT: B 513 GLN cc_start: 0.9340 (tp-100) cc_final: 0.8947 (tp40) REVERT: B 528 MET cc_start: 0.8335 (mmp) cc_final: 0.7903 (tpp) REVERT: B 537 PHE cc_start: 0.9436 (t80) cc_final: 0.8110 (t80) REVERT: B 538 LEU cc_start: 0.9151 (mp) cc_final: 0.8645 (mp) REVERT: B 541 ILE cc_start: 0.8780 (pt) cc_final: 0.8415 (pt) REVERT: B 554 MET cc_start: 0.8855 (tpt) cc_final: 0.8634 (tpt) REVERT: B 569 LEU cc_start: 0.9821 (tp) cc_final: 0.9602 (tp) REVERT: B 570 MET cc_start: 0.9430 (mmm) cc_final: 0.9163 (mmm) REVERT: B 574 LEU cc_start: 0.9806 (tp) cc_final: 0.9521 (tp) REVERT: B 605 GLU cc_start: 0.8813 (tt0) cc_final: 0.8550 (tt0) REVERT: C 35 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8831 (mp0) REVERT: C 93 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8942 (pm20) REVERT: C 96 MET cc_start: 0.9268 (mmt) cc_final: 0.8933 (mmm) REVERT: C 204 ILE cc_start: 0.9548 (mt) cc_final: 0.9271 (mt) REVERT: C 206 GLN cc_start: 0.9308 (mm-40) cc_final: 0.8708 (mm-40) REVERT: C 209 LYS cc_start: 0.8758 (mttt) cc_final: 0.8124 (ttmt) REVERT: C 215 MET cc_start: 0.9392 (mmp) cc_final: 0.9121 (mmm) REVERT: C 245 LYS cc_start: 0.8996 (mttt) cc_final: 0.8445 (ptpp) REVERT: C 246 LEU cc_start: 0.9632 (tp) cc_final: 0.9404 (tp) REVERT: C 255 MET cc_start: 0.9136 (tpt) cc_final: 0.8869 (tpp) REVERT: C 260 MET cc_start: 0.9425 (mmp) cc_final: 0.8875 (mmp) REVERT: C 300 LYS cc_start: 0.9137 (mttt) cc_final: 0.8650 (mppt) REVERT: C 301 LYS cc_start: 0.9379 (tptp) cc_final: 0.9112 (ttpt) REVERT: C 306 GLN cc_start: 0.8934 (pt0) cc_final: 0.8664 (pm20) REVERT: C 343 PHE cc_start: 0.9591 (t80) cc_final: 0.9338 (t80) REVERT: C 403 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8952 (tp30) REVERT: C 410 MET cc_start: 0.9384 (tmm) cc_final: 0.8755 (tmm) REVERT: C 454 MET cc_start: 0.9463 (tpp) cc_final: 0.8633 (tpp) REVERT: C 458 LEU cc_start: 0.9744 (mm) cc_final: 0.9429 (mm) REVERT: C 463 CYS cc_start: 0.9271 (m) cc_final: 0.9020 (m) REVERT: C 483 GLN cc_start: 0.9721 (tt0) cc_final: 0.9399 (tt0) REVERT: C 497 MET cc_start: 0.9190 (ttp) cc_final: 0.8652 (tmm) REVERT: C 538 LEU cc_start: 0.9250 (mp) cc_final: 0.8596 (mp) REVERT: C 569 LEU cc_start: 0.9808 (tp) cc_final: 0.9589 (tp) REVERT: C 593 TRP cc_start: 0.9273 (t60) cc_final: 0.8836 (t60) REVERT: D 35 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8845 (mt-10) REVERT: D 42 LYS cc_start: 0.9208 (tttt) cc_final: 0.8929 (pttm) REVERT: D 93 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9007 (pm20) REVERT: D 96 MET cc_start: 0.9315 (mmp) cc_final: 0.8856 (mmp) REVERT: D 99 MET cc_start: 0.9004 (mtm) cc_final: 0.8697 (ptp) REVERT: D 113 GLU cc_start: 0.9553 (tt0) cc_final: 0.9252 (tm-30) REVERT: D 182 LEU cc_start: 0.9799 (mm) cc_final: 0.9545 (mm) REVERT: D 198 THR cc_start: 0.9597 (t) cc_final: 0.9363 (m) REVERT: D 204 ILE cc_start: 0.9575 (mt) cc_final: 0.9301 (mt) REVERT: D 206 GLN cc_start: 0.9416 (mm-40) cc_final: 0.8977 (mm110) REVERT: D 209 LYS cc_start: 0.8598 (mttt) cc_final: 0.8181 (ttmt) REVERT: D 215 MET cc_start: 0.9421 (mmp) cc_final: 0.9144 (mmm) REVERT: D 246 LEU cc_start: 0.9706 (tp) cc_final: 0.9411 (tp) REVERT: D 250 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8362 (mm-30) REVERT: D 260 MET cc_start: 0.9650 (tpt) cc_final: 0.9418 (mmm) REVERT: D 300 LYS cc_start: 0.8988 (mttt) cc_final: 0.8500 (mppt) REVERT: D 403 GLU cc_start: 0.9364 (mm-30) cc_final: 0.8883 (tp30) REVERT: D 410 MET cc_start: 0.9324 (tpt) cc_final: 0.8613 (tpp) REVERT: D 440 MET cc_start: 0.8327 (mmm) cc_final: 0.8048 (mmm) REVERT: D 442 MET cc_start: 0.9604 (ptm) cc_final: 0.9163 (tmm) REVERT: D 445 ILE cc_start: 0.8518 (tp) cc_final: 0.8306 (tp) REVERT: D 463 CYS cc_start: 0.9356 (m) cc_final: 0.9099 (m) REVERT: D 483 GLN cc_start: 0.9729 (tt0) cc_final: 0.9372 (tt0) REVERT: D 494 CYS cc_start: 0.9112 (t) cc_final: 0.8772 (p) REVERT: D 497 MET cc_start: 0.8824 (tmm) cc_final: 0.8591 (tmm) REVERT: D 536 LEU cc_start: 0.9769 (mt) cc_final: 0.9549 (mt) REVERT: D 570 MET cc_start: 0.9213 (mmp) cc_final: 0.8881 (mmm) REVERT: D 574 LEU cc_start: 0.9711 (tp) cc_final: 0.9443 (tp) REVERT: D 577 MET cc_start: 0.8817 (ppp) cc_final: 0.8293 (ppp) REVERT: D 593 TRP cc_start: 0.9293 (t60) cc_final: 0.8633 (t60) REVERT: D 605 GLU cc_start: 0.9140 (tt0) cc_final: 0.8906 (tt0) REVERT: D 629 TRP cc_start: 0.8789 (m100) cc_final: 0.8398 (m-10) outliers start: 0 outliers final: 0 residues processed: 862 average time/residue: 0.2877 time to fit residues: 399.1641 Evaluate side-chains 691 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 0.0470 chunk 3 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 204 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 122 optimal weight: 0.0020 chunk 215 optimal weight: 6.9990 chunk 60 optimal weight: 0.0030 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 582 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20602 Z= 0.154 Angle : 0.689 9.511 27945 Z= 0.332 Chirality : 0.043 0.167 3138 Planarity : 0.004 0.059 3522 Dihedral : 8.040 104.054 2798 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2472 helix: -0.39 (0.14), residues: 1372 sheet: -3.81 (0.60), residues: 48 loop : -2.71 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 613 HIS 0.006 0.001 HIS A 84 PHE 0.021 0.001 PHE D 537 TYR 0.030 0.001 TYR A 270 ARG 0.006 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8764 (mt-10) REVERT: A 93 GLU cc_start: 0.9327 (mt-10) cc_final: 0.8906 (pm20) REVERT: A 113 GLU cc_start: 0.9364 (tt0) cc_final: 0.8931 (tm-30) REVERT: A 146 ARG cc_start: 0.9432 (mtt180) cc_final: 0.8970 (mmm-85) REVERT: A 198 THR cc_start: 0.9670 (t) cc_final: 0.9075 (m) REVERT: A 201 HIS cc_start: 0.9415 (m90) cc_final: 0.8967 (m90) REVERT: A 206 GLN cc_start: 0.9441 (mm-40) cc_final: 0.8927 (mm110) REVERT: A 215 MET cc_start: 0.9480 (mmm) cc_final: 0.9137 (mmm) REVERT: A 245 LYS cc_start: 0.8548 (mttt) cc_final: 0.8091 (mtpp) REVERT: A 246 LEU cc_start: 0.9705 (tp) cc_final: 0.9487 (tp) REVERT: A 250 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8559 (mm-30) REVERT: A 255 MET cc_start: 0.9289 (mmm) cc_final: 0.8976 (tpp) REVERT: A 260 MET cc_start: 0.9611 (tpt) cc_final: 0.9306 (mmm) REVERT: A 297 ILE cc_start: 0.9446 (mm) cc_final: 0.9127 (tp) REVERT: A 300 LYS cc_start: 0.9109 (mttt) cc_final: 0.8603 (mppt) REVERT: A 306 GLN cc_start: 0.9063 (pt0) cc_final: 0.8688 (pm20) REVERT: A 307 ILE cc_start: 0.9126 (mt) cc_final: 0.8920 (mt) REVERT: A 403 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8886 (tp30) REVERT: A 410 MET cc_start: 0.9181 (tpt) cc_final: 0.8559 (tpp) REVERT: A 421 LEU cc_start: 0.9185 (tp) cc_final: 0.8963 (tp) REVERT: A 440 MET cc_start: 0.7971 (mmm) cc_final: 0.7549 (mmm) REVERT: A 454 MET cc_start: 0.9124 (mtt) cc_final: 0.8828 (mmm) REVERT: A 463 CYS cc_start: 0.9489 (m) cc_final: 0.9134 (m) REVERT: A 483 GLN cc_start: 0.9702 (tt0) cc_final: 0.9299 (tp40) REVERT: A 497 MET cc_start: 0.9328 (ttp) cc_final: 0.8833 (ttp) REVERT: A 518 GLU cc_start: 0.9083 (mp0) cc_final: 0.8828 (mp0) REVERT: A 537 PHE cc_start: 0.9588 (t80) cc_final: 0.8481 (t80) REVERT: A 538 LEU cc_start: 0.9230 (mp) cc_final: 0.8979 (mp) REVERT: A 541 ILE cc_start: 0.8764 (pt) cc_final: 0.8349 (mm) REVERT: A 551 LEU cc_start: 0.8082 (mt) cc_final: 0.7797 (mp) REVERT: A 554 MET cc_start: 0.9237 (ppp) cc_final: 0.8825 (ppp) REVERT: A 570 MET cc_start: 0.9331 (mmp) cc_final: 0.9010 (mmm) REVERT: A 580 ASP cc_start: 0.9004 (m-30) cc_final: 0.8515 (m-30) REVERT: A 605 GLU cc_start: 0.9260 (tt0) cc_final: 0.8997 (tt0) REVERT: B 57 ASP cc_start: 0.9200 (m-30) cc_final: 0.8889 (m-30) REVERT: B 70 CYS cc_start: 0.8481 (p) cc_final: 0.8003 (p) REVERT: B 96 MET cc_start: 0.9625 (mmt) cc_final: 0.9278 (mmp) REVERT: B 99 MET cc_start: 0.9251 (mtp) cc_final: 0.8695 (tpp) REVERT: B 113 GLU cc_start: 0.9505 (tt0) cc_final: 0.9057 (tm-30) REVERT: B 118 GLN cc_start: 0.9474 (tt0) cc_final: 0.9150 (tm-30) REVERT: B 122 HIS cc_start: 0.9621 (m170) cc_final: 0.9290 (m-70) REVERT: B 123 ILE cc_start: 0.9629 (mt) cc_final: 0.9304 (mt) REVERT: B 128 GLN cc_start: 0.9151 (pt0) cc_final: 0.8349 (tm-30) REVERT: B 161 TYR cc_start: 0.8620 (t80) cc_final: 0.8236 (t80) REVERT: B 204 ILE cc_start: 0.9465 (mt) cc_final: 0.9228 (tp) REVERT: B 209 LYS cc_start: 0.9200 (mttt) cc_final: 0.8654 (ttmt) REVERT: B 245 LYS cc_start: 0.9415 (mttt) cc_final: 0.8920 (ptpp) REVERT: B 246 LEU cc_start: 0.9581 (tp) cc_final: 0.9351 (tp) REVERT: B 260 MET cc_start: 0.9591 (mmm) cc_final: 0.9145 (mmm) REVERT: B 294 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8776 (mt-10) REVERT: B 300 LYS cc_start: 0.9043 (mttt) cc_final: 0.8530 (mppt) REVERT: B 303 GLU cc_start: 0.8982 (tp30) cc_final: 0.8414 (tp30) REVERT: B 306 GLN cc_start: 0.8812 (pt0) cc_final: 0.8409 (pm20) REVERT: B 403 GLU cc_start: 0.9050 (tp30) cc_final: 0.8818 (tp30) REVERT: B 454 MET cc_start: 0.9395 (mmt) cc_final: 0.8764 (tpp) REVERT: B 483 GLN cc_start: 0.9719 (tt0) cc_final: 0.9121 (tp40) REVERT: B 490 LEU cc_start: 0.9717 (tt) cc_final: 0.9507 (tt) REVERT: B 494 CYS cc_start: 0.8927 (t) cc_final: 0.8697 (p) REVERT: B 497 MET cc_start: 0.9308 (ttp) cc_final: 0.8621 (ttp) REVERT: B 513 GLN cc_start: 0.9361 (tp-100) cc_final: 0.9017 (tp40) REVERT: B 528 MET cc_start: 0.8314 (mmp) cc_final: 0.7489 (mmm) REVERT: B 537 PHE cc_start: 0.9440 (t80) cc_final: 0.8092 (t80) REVERT: B 538 LEU cc_start: 0.9138 (mp) cc_final: 0.8881 (mp) REVERT: B 541 ILE cc_start: 0.8806 (pt) cc_final: 0.8468 (pt) REVERT: B 554 MET cc_start: 0.8860 (tpt) cc_final: 0.8619 (tpt) REVERT: B 570 MET cc_start: 0.9428 (mmm) cc_final: 0.9182 (mmm) REVERT: B 574 LEU cc_start: 0.9801 (tp) cc_final: 0.9553 (tp) REVERT: B 605 GLU cc_start: 0.8842 (tt0) cc_final: 0.8587 (tt0) REVERT: C 35 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8872 (mp0) REVERT: C 93 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8928 (pm20) REVERT: C 96 MET cc_start: 0.9259 (mmt) cc_final: 0.8926 (mmm) REVERT: C 182 LEU cc_start: 0.9748 (mm) cc_final: 0.9535 (tp) REVERT: C 204 ILE cc_start: 0.9550 (mt) cc_final: 0.9263 (mt) REVERT: C 209 LYS cc_start: 0.8741 (mttt) cc_final: 0.8039 (ttmt) REVERT: C 215 MET cc_start: 0.9382 (mmp) cc_final: 0.9111 (mmm) REVERT: C 245 LYS cc_start: 0.9033 (mttt) cc_final: 0.8440 (ptpp) REVERT: C 246 LEU cc_start: 0.9626 (tp) cc_final: 0.9397 (tp) REVERT: C 260 MET cc_start: 0.9426 (mmp) cc_final: 0.8912 (mmp) REVERT: C 294 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8674 (mt-10) REVERT: C 300 LYS cc_start: 0.9182 (mttt) cc_final: 0.8689 (mppt) REVERT: C 301 LYS cc_start: 0.9388 (tptp) cc_final: 0.8982 (ttmt) REVERT: C 403 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8944 (tp30) REVERT: C 442 MET cc_start: 0.9592 (ttp) cc_final: 0.9360 (tmm) REVERT: C 454 MET cc_start: 0.9462 (tpp) cc_final: 0.9189 (mmt) REVERT: C 463 CYS cc_start: 0.9314 (m) cc_final: 0.9034 (m) REVERT: C 483 GLN cc_start: 0.9713 (tt0) cc_final: 0.9411 (tt0) REVERT: C 497 MET cc_start: 0.9251 (ttp) cc_final: 0.8656 (tmm) REVERT: C 537 PHE cc_start: 0.9559 (t80) cc_final: 0.9301 (t80) REVERT: C 538 LEU cc_start: 0.9053 (mp) cc_final: 0.8575 (mp) REVERT: C 570 MET cc_start: 0.9341 (mmp) cc_final: 0.9028 (mmm) REVERT: C 593 TRP cc_start: 0.9288 (t60) cc_final: 0.8871 (t60) REVERT: D 35 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8842 (mt-10) REVERT: D 42 LYS cc_start: 0.9216 (tttt) cc_final: 0.8916 (pttm) REVERT: D 93 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8950 (pm20) REVERT: D 96 MET cc_start: 0.9349 (mmp) cc_final: 0.8906 (mmm) REVERT: D 99 MET cc_start: 0.8969 (mtm) cc_final: 0.8669 (ptp) REVERT: D 113 GLU cc_start: 0.9563 (tt0) cc_final: 0.9252 (tm-30) REVERT: D 204 ILE cc_start: 0.9564 (mt) cc_final: 0.9292 (mt) REVERT: D 206 GLN cc_start: 0.9453 (mm-40) cc_final: 0.8905 (mm-40) REVERT: D 209 LYS cc_start: 0.8537 (mttt) cc_final: 0.8117 (mtpt) REVERT: D 215 MET cc_start: 0.9431 (mmp) cc_final: 0.9144 (mmm) REVERT: D 229 LEU cc_start: 0.9054 (mp) cc_final: 0.8710 (pp) REVERT: D 245 LYS cc_start: 0.8957 (mttt) cc_final: 0.8321 (ptpp) REVERT: D 246 LEU cc_start: 0.9698 (tp) cc_final: 0.9447 (tp) REVERT: D 250 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8518 (mm-30) REVERT: D 260 MET cc_start: 0.9663 (tpt) cc_final: 0.9397 (mmm) REVERT: D 300 LYS cc_start: 0.8994 (mttt) cc_final: 0.8503 (mppt) REVERT: D 301 LYS cc_start: 0.9417 (tptp) cc_final: 0.9108 (tmtt) REVERT: D 332 LEU cc_start: 0.8894 (mm) cc_final: 0.8626 (pp) REVERT: D 343 PHE cc_start: 0.9511 (t80) cc_final: 0.9266 (t80) REVERT: D 347 CYS cc_start: 0.8514 (m) cc_final: 0.8123 (m) REVERT: D 399 ILE cc_start: 0.8524 (mm) cc_final: 0.8234 (mm) REVERT: D 403 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8842 (tp30) REVERT: D 410 MET cc_start: 0.9323 (tpt) cc_final: 0.9080 (mmm) REVERT: D 440 MET cc_start: 0.8571 (mmm) cc_final: 0.8086 (mmm) REVERT: D 454 MET cc_start: 0.9164 (mmt) cc_final: 0.8876 (mmm) REVERT: D 463 CYS cc_start: 0.9396 (m) cc_final: 0.9092 (m) REVERT: D 483 GLN cc_start: 0.9726 (tt0) cc_final: 0.9390 (tp40) REVERT: D 494 CYS cc_start: 0.9065 (t) cc_final: 0.8842 (p) REVERT: D 497 MET cc_start: 0.8780 (tmm) cc_final: 0.8572 (tmm) REVERT: D 536 LEU cc_start: 0.9759 (mt) cc_final: 0.9545 (mt) REVERT: D 570 MET cc_start: 0.9127 (mmp) cc_final: 0.8898 (mmm) REVERT: D 577 MET cc_start: 0.8726 (ppp) cc_final: 0.8482 (ppp) REVERT: D 593 TRP cc_start: 0.9303 (t60) cc_final: 0.8703 (t60) REVERT: D 629 TRP cc_start: 0.8765 (m100) cc_final: 0.8294 (m-10) outliers start: 0 outliers final: 0 residues processed: 840 average time/residue: 0.2710 time to fit residues: 363.0144 Evaluate side-chains 683 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20602 Z= 0.204 Angle : 0.691 9.749 27945 Z= 0.344 Chirality : 0.044 0.168 3138 Planarity : 0.004 0.057 3522 Dihedral : 7.843 106.508 2798 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2472 helix: -0.46 (0.14), residues: 1428 sheet: -3.81 (0.59), residues: 48 loop : -2.69 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 583 HIS 0.008 0.001 HIS D 582 PHE 0.014 0.001 PHE D 537 TYR 0.014 0.001 TYR C 526 ARG 0.004 0.000 ARG A 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 787 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.9524 (m-30) cc_final: 0.9314 (m-30) REVERT: A 39 LEU cc_start: 0.9602 (tp) cc_final: 0.9329 (tp) REVERT: A 42 LYS cc_start: 0.9417 (tttt) cc_final: 0.9042 (ttpt) REVERT: A 93 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8744 (pm20) REVERT: A 113 GLU cc_start: 0.9382 (tt0) cc_final: 0.8950 (tm-30) REVERT: A 146 ARG cc_start: 0.9463 (mtt180) cc_final: 0.9015 (mmm-85) REVERT: A 182 LEU cc_start: 0.9739 (mm) cc_final: 0.9380 (mm) REVERT: A 201 HIS cc_start: 0.9482 (m90) cc_final: 0.8972 (m90) REVERT: A 206 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9047 (mm110) REVERT: A 215 MET cc_start: 0.9494 (mmm) cc_final: 0.9162 (mmm) REVERT: A 245 LYS cc_start: 0.8676 (mttt) cc_final: 0.8190 (mtpp) REVERT: A 246 LEU cc_start: 0.9715 (tp) cc_final: 0.9487 (tp) REVERT: A 250 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 260 MET cc_start: 0.9644 (tpt) cc_final: 0.9353 (mmm) REVERT: A 300 LYS cc_start: 0.9235 (mttt) cc_final: 0.8725 (mppt) REVERT: A 301 LYS cc_start: 0.9300 (tptp) cc_final: 0.8956 (tptt) REVERT: A 403 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9001 (tp30) REVERT: A 410 MET cc_start: 0.9149 (tpt) cc_final: 0.8064 (tpp) REVERT: A 440 MET cc_start: 0.8054 (mmm) cc_final: 0.7602 (mmm) REVERT: A 454 MET cc_start: 0.9200 (mtt) cc_final: 0.8888 (mmm) REVERT: A 463 CYS cc_start: 0.9473 (m) cc_final: 0.9215 (m) REVERT: A 483 GLN cc_start: 0.9723 (tt0) cc_final: 0.9321 (tp40) REVERT: A 497 MET cc_start: 0.9343 (ttp) cc_final: 0.8868 (ttp) REVERT: A 526 TYR cc_start: 0.8741 (t80) cc_final: 0.8326 (t80) REVERT: A 537 PHE cc_start: 0.9596 (t80) cc_final: 0.8598 (t80) REVERT: A 538 LEU cc_start: 0.9236 (mp) cc_final: 0.9012 (mp) REVERT: A 554 MET cc_start: 0.9288 (ppp) cc_final: 0.8742 (ppp) REVERT: A 570 MET cc_start: 0.9374 (mmp) cc_final: 0.9059 (mmm) REVERT: A 580 ASP cc_start: 0.8894 (m-30) cc_final: 0.8394 (m-30) REVERT: A 605 GLU cc_start: 0.9322 (tt0) cc_final: 0.9067 (tt0) REVERT: B 50 LEU cc_start: 0.9232 (mp) cc_final: 0.8682 (tp) REVERT: B 57 ASP cc_start: 0.9207 (m-30) cc_final: 0.8880 (m-30) REVERT: B 70 CYS cc_start: 0.8474 (p) cc_final: 0.7984 (p) REVERT: B 96 MET cc_start: 0.9630 (mmt) cc_final: 0.9278 (mmp) REVERT: B 99 MET cc_start: 0.9219 (mtp) cc_final: 0.8776 (tpp) REVERT: B 113 GLU cc_start: 0.9513 (tt0) cc_final: 0.9127 (tm-30) REVERT: B 118 GLN cc_start: 0.9492 (tt0) cc_final: 0.9188 (tm-30) REVERT: B 123 ILE cc_start: 0.9627 (mt) cc_final: 0.9277 (mt) REVERT: B 128 GLN cc_start: 0.9063 (pt0) cc_final: 0.8176 (tm-30) REVERT: B 181 LEU cc_start: 0.9708 (tp) cc_final: 0.9399 (pp) REVERT: B 182 LEU cc_start: 0.9799 (mm) cc_final: 0.9575 (mm) REVERT: B 209 LYS cc_start: 0.9186 (mttt) cc_final: 0.8611 (ttmt) REVERT: B 246 LEU cc_start: 0.9610 (tp) cc_final: 0.9380 (tp) REVERT: B 260 MET cc_start: 0.9611 (mmm) cc_final: 0.9174 (mmm) REVERT: B 293 LEU cc_start: 0.9765 (mt) cc_final: 0.9494 (pp) REVERT: B 294 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 300 LYS cc_start: 0.9054 (mttt) cc_final: 0.8526 (mppt) REVERT: B 306 GLN cc_start: 0.8824 (pt0) cc_final: 0.8495 (mp10) REVERT: B 403 GLU cc_start: 0.9048 (tp30) cc_final: 0.8734 (tp30) REVERT: B 450 GLU cc_start: 0.9284 (pm20) cc_final: 0.8895 (pm20) REVERT: B 454 MET cc_start: 0.9443 (mmt) cc_final: 0.8845 (tpp) REVERT: B 463 CYS cc_start: 0.9469 (m) cc_final: 0.9265 (m) REVERT: B 483 GLN cc_start: 0.9717 (tt0) cc_final: 0.9384 (tp40) REVERT: B 497 MET cc_start: 0.9324 (ttp) cc_final: 0.8794 (ttp) REVERT: B 513 GLN cc_start: 0.9406 (tp-100) cc_final: 0.9012 (tp40) REVERT: B 528 MET cc_start: 0.8342 (mmp) cc_final: 0.7502 (mmm) REVERT: B 537 PHE cc_start: 0.9476 (t80) cc_final: 0.8172 (t80) REVERT: B 538 LEU cc_start: 0.9170 (mp) cc_final: 0.8879 (mp) REVERT: B 541 ILE cc_start: 0.8883 (pt) cc_final: 0.8568 (pt) REVERT: B 570 MET cc_start: 0.9456 (mmm) cc_final: 0.9202 (mmm) REVERT: B 574 LEU cc_start: 0.9808 (tp) cc_final: 0.9565 (tp) REVERT: B 593 TRP cc_start: 0.9404 (t60) cc_final: 0.8884 (t60) REVERT: B 605 GLU cc_start: 0.8934 (tt0) cc_final: 0.8708 (tt0) REVERT: C 34 ASP cc_start: 0.9412 (m-30) cc_final: 0.9199 (m-30) REVERT: C 35 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8912 (mp0) REVERT: C 93 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9000 (pm20) REVERT: C 96 MET cc_start: 0.9285 (mmt) cc_final: 0.8949 (mmm) REVERT: C 204 ILE cc_start: 0.9577 (mt) cc_final: 0.9332 (mt) REVERT: C 206 GLN cc_start: 0.9378 (mm-40) cc_final: 0.8792 (mm-40) REVERT: C 209 LYS cc_start: 0.8762 (mttt) cc_final: 0.8065 (ttmt) REVERT: C 215 MET cc_start: 0.9392 (mmp) cc_final: 0.9078 (mmm) REVERT: C 245 LYS cc_start: 0.9083 (mttt) cc_final: 0.8490 (ptpp) REVERT: C 246 LEU cc_start: 0.9621 (tp) cc_final: 0.9408 (tp) REVERT: C 260 MET cc_start: 0.9448 (mmp) cc_final: 0.8942 (mmp) REVERT: C 294 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8643 (mt-10) REVERT: C 300 LYS cc_start: 0.9219 (mttt) cc_final: 0.8681 (mppt) REVERT: C 301 LYS cc_start: 0.9399 (tptp) cc_final: 0.9097 (ttpt) REVERT: C 343 PHE cc_start: 0.9634 (t80) cc_final: 0.9433 (t80) REVERT: C 403 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8975 (tp30) REVERT: C 442 MET cc_start: 0.9632 (ttp) cc_final: 0.9375 (tmm) REVERT: C 454 MET cc_start: 0.9482 (tpp) cc_final: 0.9279 (mmt) REVERT: C 463 CYS cc_start: 0.9342 (m) cc_final: 0.9107 (m) REVERT: C 483 GLN cc_start: 0.9716 (tt0) cc_final: 0.9450 (tt0) REVERT: C 497 MET cc_start: 0.9236 (ttp) cc_final: 0.8558 (tmm) REVERT: C 537 PHE cc_start: 0.9556 (t80) cc_final: 0.9230 (t80) REVERT: C 569 LEU cc_start: 0.9797 (tp) cc_final: 0.9587 (tp) REVERT: C 570 MET cc_start: 0.9406 (mmp) cc_final: 0.9068 (mmm) REVERT: C 593 TRP cc_start: 0.9300 (t60) cc_final: 0.8628 (t60) REVERT: D 35 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8835 (mt-10) REVERT: D 42 LYS cc_start: 0.9233 (tttt) cc_final: 0.8931 (pttm) REVERT: D 96 MET cc_start: 0.9398 (mmp) cc_final: 0.8918 (mmp) REVERT: D 99 MET cc_start: 0.8993 (mtm) cc_final: 0.8626 (ptp) REVERT: D 113 GLU cc_start: 0.9552 (tt0) cc_final: 0.9239 (tm-30) REVERT: D 204 ILE cc_start: 0.9584 (mt) cc_final: 0.9302 (mt) REVERT: D 206 GLN cc_start: 0.9455 (mm-40) cc_final: 0.8922 (mm-40) REVERT: D 209 LYS cc_start: 0.8553 (mttt) cc_final: 0.8068 (ttmt) REVERT: D 215 MET cc_start: 0.9458 (mmp) cc_final: 0.9157 (mmm) REVERT: D 245 LYS cc_start: 0.9025 (mttt) cc_final: 0.8380 (ptpp) REVERT: D 246 LEU cc_start: 0.9695 (tp) cc_final: 0.9445 (tp) REVERT: D 250 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8554 (mm-30) REVERT: D 260 MET cc_start: 0.9676 (tpt) cc_final: 0.9423 (mmm) REVERT: D 297 ILE cc_start: 0.9483 (tp) cc_final: 0.9275 (tp) REVERT: D 300 LYS cc_start: 0.9032 (mttt) cc_final: 0.8599 (mppt) REVERT: D 301 LYS cc_start: 0.9332 (tptp) cc_final: 0.8992 (tmtt) REVERT: D 343 PHE cc_start: 0.9550 (t80) cc_final: 0.9300 (t80) REVERT: D 403 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8932 (tp30) REVERT: D 421 LEU cc_start: 0.9463 (tp) cc_final: 0.9239 (tp) REVERT: D 440 MET cc_start: 0.8600 (mmm) cc_final: 0.8119 (mmm) REVERT: D 442 MET cc_start: 0.9702 (ttp) cc_final: 0.9312 (tmm) REVERT: D 445 ILE cc_start: 0.8524 (tp) cc_final: 0.8315 (tp) REVERT: D 454 MET cc_start: 0.9252 (mmt) cc_final: 0.8948 (mmm) REVERT: D 463 CYS cc_start: 0.9419 (m) cc_final: 0.9147 (m) REVERT: D 483 GLN cc_start: 0.9730 (tt0) cc_final: 0.9421 (tp40) REVERT: D 485 MET cc_start: 0.9608 (mmm) cc_final: 0.8313 (mmm) REVERT: D 497 MET cc_start: 0.8863 (tmm) cc_final: 0.8292 (tmm) REVERT: D 536 LEU cc_start: 0.9752 (mt) cc_final: 0.9544 (mt) REVERT: D 570 MET cc_start: 0.9244 (mmp) cc_final: 0.8971 (mmm) REVERT: D 577 MET cc_start: 0.8878 (ppp) cc_final: 0.8639 (ppp) REVERT: D 593 TRP cc_start: 0.9330 (t60) cc_final: 0.8772 (t60) REVERT: D 605 GLU cc_start: 0.9232 (tt0) cc_final: 0.9003 (tt0) outliers start: 0 outliers final: 0 residues processed: 787 average time/residue: 0.2774 time to fit residues: 346.8706 Evaluate side-chains 664 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 664 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.0000 chunk 27 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 582 HIS ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20602 Z= 0.230 Angle : 0.712 13.202 27945 Z= 0.355 Chirality : 0.044 0.169 3138 Planarity : 0.004 0.057 3522 Dihedral : 7.637 107.318 2798 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2472 helix: -0.45 (0.13), residues: 1432 sheet: -3.88 (0.57), residues: 48 loop : -2.70 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 583 HIS 0.008 0.001 HIS B 84 PHE 0.015 0.001 PHE D 504 TYR 0.017 0.001 TYR C 526 ARG 0.012 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9726 (mp) cc_final: 0.9509 (mp) REVERT: A 39 LEU cc_start: 0.9605 (tp) cc_final: 0.9350 (tp) REVERT: A 42 LYS cc_start: 0.9445 (tttt) cc_final: 0.9067 (ttpt) REVERT: A 93 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8700 (pm20) REVERT: A 113 GLU cc_start: 0.9358 (tt0) cc_final: 0.8909 (tm-30) REVERT: A 201 HIS cc_start: 0.9366 (m90) cc_final: 0.8981 (m90) REVERT: A 206 GLN cc_start: 0.9462 (mm-40) cc_final: 0.9033 (mm110) REVERT: A 215 MET cc_start: 0.9486 (mmm) cc_final: 0.9142 (mmm) REVERT: A 245 LYS cc_start: 0.8839 (mttt) cc_final: 0.8386 (mttm) REVERT: A 246 LEU cc_start: 0.9710 (tp) cc_final: 0.9507 (tp) REVERT: A 250 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8616 (mm-30) REVERT: A 260 MET cc_start: 0.9646 (tpt) cc_final: 0.9402 (mmm) REVERT: A 300 LYS cc_start: 0.9267 (mttt) cc_final: 0.8776 (mppt) REVERT: A 301 LYS cc_start: 0.9311 (tptp) cc_final: 0.8998 (tptp) REVERT: A 305 ARG cc_start: 0.9029 (ptp-110) cc_final: 0.8801 (ptp-110) REVERT: A 343 PHE cc_start: 0.9653 (t80) cc_final: 0.9379 (t80) REVERT: A 403 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9029 (tp30) REVERT: A 410 MET cc_start: 0.9011 (tpt) cc_final: 0.8282 (tpp) REVERT: A 435 MET cc_start: 0.8950 (mmt) cc_final: 0.8719 (mmp) REVERT: A 440 MET cc_start: 0.8053 (mmm) cc_final: 0.7590 (mmm) REVERT: A 454 MET cc_start: 0.9257 (mtt) cc_final: 0.8668 (tpp) REVERT: A 463 CYS cc_start: 0.9518 (m) cc_final: 0.9315 (m) REVERT: A 497 MET cc_start: 0.9336 (ttp) cc_final: 0.8869 (ttp) REVERT: A 526 TYR cc_start: 0.8756 (t80) cc_final: 0.8440 (t80) REVERT: A 537 PHE cc_start: 0.9594 (t80) cc_final: 0.8619 (t80) REVERT: A 538 LEU cc_start: 0.9231 (mp) cc_final: 0.9025 (mp) REVERT: A 554 MET cc_start: 0.9375 (ppp) cc_final: 0.8797 (ppp) REVERT: A 570 MET cc_start: 0.9459 (mmp) cc_final: 0.9077 (mmm) REVERT: A 580 ASP cc_start: 0.8931 (m-30) cc_final: 0.8445 (m-30) REVERT: A 605 GLU cc_start: 0.9377 (tt0) cc_final: 0.9116 (tt0) REVERT: B 57 ASP cc_start: 0.9211 (m-30) cc_final: 0.8891 (m-30) REVERT: B 70 CYS cc_start: 0.8490 (p) cc_final: 0.7915 (p) REVERT: B 96 MET cc_start: 0.9653 (mmt) cc_final: 0.9309 (mmp) REVERT: B 99 MET cc_start: 0.9261 (mtp) cc_final: 0.8896 (tpp) REVERT: B 105 LEU cc_start: 0.9512 (tp) cc_final: 0.9199 (tp) REVERT: B 113 GLU cc_start: 0.9483 (tt0) cc_final: 0.9028 (tm-30) REVERT: B 118 GLN cc_start: 0.9516 (tt0) cc_final: 0.9163 (tm-30) REVERT: B 123 ILE cc_start: 0.9647 (mt) cc_final: 0.9303 (mt) REVERT: B 128 GLN cc_start: 0.9016 (pt0) cc_final: 0.8195 (tm-30) REVERT: B 181 LEU cc_start: 0.9728 (tp) cc_final: 0.9455 (pp) REVERT: B 182 LEU cc_start: 0.9807 (mm) cc_final: 0.9537 (mm) REVERT: B 209 LYS cc_start: 0.9146 (mttt) cc_final: 0.8570 (ttmt) REVERT: B 245 LYS cc_start: 0.9351 (mttt) cc_final: 0.8858 (ptpp) REVERT: B 260 MET cc_start: 0.9626 (mmm) cc_final: 0.9135 (mmm) REVERT: B 293 LEU cc_start: 0.9763 (mt) cc_final: 0.9511 (pp) REVERT: B 297 ILE cc_start: 0.9543 (pt) cc_final: 0.9314 (tp) REVERT: B 300 LYS cc_start: 0.9083 (mttt) cc_final: 0.8550 (mppt) REVERT: B 301 LYS cc_start: 0.9099 (tptp) cc_final: 0.8866 (tptp) REVERT: B 306 GLN cc_start: 0.8815 (pt0) cc_final: 0.8565 (mp10) REVERT: B 323 ARG cc_start: 0.8719 (ptp-170) cc_final: 0.8462 (ptp-170) REVERT: B 403 GLU cc_start: 0.9105 (tp30) cc_final: 0.8734 (tp30) REVERT: B 421 LEU cc_start: 0.9410 (tp) cc_final: 0.8883 (tp) REVERT: B 440 MET cc_start: 0.9405 (tpp) cc_final: 0.9185 (tpp) REVERT: B 442 MET cc_start: 0.9237 (ptm) cc_final: 0.8977 (ppp) REVERT: B 454 MET cc_start: 0.9444 (mmt) cc_final: 0.8840 (tpp) REVERT: B 463 CYS cc_start: 0.9480 (m) cc_final: 0.9229 (m) REVERT: B 483 GLN cc_start: 0.9734 (tt0) cc_final: 0.9192 (tp40) REVERT: B 497 MET cc_start: 0.9380 (ttp) cc_final: 0.8860 (ttp) REVERT: B 513 GLN cc_start: 0.9436 (tp-100) cc_final: 0.9013 (tp40) REVERT: B 528 MET cc_start: 0.8289 (mmp) cc_final: 0.7465 (mmm) REVERT: B 537 PHE cc_start: 0.9486 (t80) cc_final: 0.8204 (t80) REVERT: B 538 LEU cc_start: 0.9180 (mp) cc_final: 0.8924 (mp) REVERT: B 541 ILE cc_start: 0.8979 (pt) cc_final: 0.8696 (pt) REVERT: B 554 MET cc_start: 0.8873 (tpt) cc_final: 0.8604 (tpt) REVERT: B 574 LEU cc_start: 0.9802 (tp) cc_final: 0.9534 (tp) REVERT: B 593 TRP cc_start: 0.9402 (t60) cc_final: 0.8919 (t60) REVERT: C 35 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9023 (mt-10) REVERT: C 93 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8953 (pm20) REVERT: C 96 MET cc_start: 0.9326 (mmt) cc_final: 0.9005 (mmp) REVERT: C 161 TYR cc_start: 0.8683 (t80) cc_final: 0.8414 (t80) REVERT: C 204 ILE cc_start: 0.9587 (mt) cc_final: 0.9341 (mt) REVERT: C 206 GLN cc_start: 0.9368 (mm-40) cc_final: 0.8810 (mm-40) REVERT: C 209 LYS cc_start: 0.8844 (mttt) cc_final: 0.8158 (ttmt) REVERT: C 215 MET cc_start: 0.9398 (mmp) cc_final: 0.9183 (mmm) REVERT: C 245 LYS cc_start: 0.9076 (mttt) cc_final: 0.8511 (ptpp) REVERT: C 246 LEU cc_start: 0.9621 (tp) cc_final: 0.9414 (tp) REVERT: C 260 MET cc_start: 0.9458 (mmp) cc_final: 0.8962 (mmp) REVERT: C 294 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8622 (mt-10) REVERT: C 300 LYS cc_start: 0.9226 (mttt) cc_final: 0.8689 (mppt) REVERT: C 301 LYS cc_start: 0.9439 (tptp) cc_final: 0.9018 (ttmt) REVERT: C 403 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8943 (tp30) REVERT: C 442 MET cc_start: 0.9676 (ttp) cc_final: 0.9430 (tmm) REVERT: C 463 CYS cc_start: 0.9308 (m) cc_final: 0.9100 (m) REVERT: C 483 GLN cc_start: 0.9709 (tt0) cc_final: 0.9169 (mm-40) REVERT: C 497 MET cc_start: 0.9226 (ttp) cc_final: 0.8742 (ttp) REVERT: C 518 GLU cc_start: 0.9231 (tm-30) cc_final: 0.9023 (tm-30) REVERT: C 537 PHE cc_start: 0.9548 (t80) cc_final: 0.8826 (t80) REVERT: C 538 LEU cc_start: 0.9081 (mp) cc_final: 0.8872 (mp) REVERT: C 570 MET cc_start: 0.9462 (mmp) cc_final: 0.9132 (mmm) REVERT: D 35 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8841 (mt-10) REVERT: D 42 LYS cc_start: 0.9224 (tttt) cc_final: 0.8896 (pttm) REVERT: D 93 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8841 (pm20) REVERT: D 99 MET cc_start: 0.9049 (mtm) cc_final: 0.8624 (ptp) REVERT: D 113 GLU cc_start: 0.9544 (tt0) cc_final: 0.9255 (tm-30) REVERT: D 204 ILE cc_start: 0.9575 (mt) cc_final: 0.9268 (mt) REVERT: D 209 LYS cc_start: 0.8578 (mttt) cc_final: 0.8106 (ttmt) REVERT: D 215 MET cc_start: 0.9456 (mmp) cc_final: 0.9097 (mmm) REVERT: D 245 LYS cc_start: 0.9082 (mttt) cc_final: 0.8529 (ptpp) REVERT: D 246 LEU cc_start: 0.9695 (tp) cc_final: 0.9449 (tp) REVERT: D 250 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8489 (mm-30) REVERT: D 260 MET cc_start: 0.9680 (tpt) cc_final: 0.9446 (mmm) REVERT: D 300 LYS cc_start: 0.9027 (mttt) cc_final: 0.8533 (mppt) REVERT: D 332 LEU cc_start: 0.8963 (mm) cc_final: 0.8726 (pp) REVERT: D 403 GLU cc_start: 0.9400 (mm-30) cc_final: 0.8993 (tp30) REVERT: D 406 ASP cc_start: 0.9370 (m-30) cc_final: 0.9135 (m-30) REVERT: D 410 MET cc_start: 0.9238 (mmp) cc_final: 0.8962 (tpp) REVERT: D 421 LEU cc_start: 0.9499 (tp) cc_final: 0.9297 (tp) REVERT: D 440 MET cc_start: 0.8652 (mmm) cc_final: 0.8125 (mmm) REVERT: D 442 MET cc_start: 0.9721 (ttp) cc_final: 0.9439 (tmm) REVERT: D 483 GLN cc_start: 0.9709 (tt0) cc_final: 0.9349 (mm-40) REVERT: D 485 MET cc_start: 0.9633 (mmm) cc_final: 0.9338 (mmm) REVERT: D 497 MET cc_start: 0.8786 (tmm) cc_final: 0.8293 (tmm) REVERT: D 570 MET cc_start: 0.9344 (mmp) cc_final: 0.9031 (mmm) REVERT: D 578 MET cc_start: 0.9273 (tpp) cc_final: 0.9036 (tpt) REVERT: D 593 TRP cc_start: 0.9322 (t60) cc_final: 0.8821 (t60) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 0.2799 time to fit residues: 346.4503 Evaluate side-chains 668 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.0000 chunk 72 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN A 267 GLN ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN C 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20602 Z= 0.184 Angle : 0.695 11.065 27945 Z= 0.338 Chirality : 0.044 0.167 3138 Planarity : 0.004 0.059 3522 Dihedral : 7.322 106.717 2798 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2472 helix: -0.29 (0.14), residues: 1408 sheet: -3.93 (0.57), residues: 48 loop : -2.58 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 583 HIS 0.009 0.001 HIS B 84 PHE 0.021 0.001 PHE C 343 TYR 0.019 0.001 TYR B 161 ARG 0.007 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9568 (tp) cc_final: 0.9316 (tp) REVERT: A 42 LYS cc_start: 0.9436 (tttt) cc_final: 0.9052 (ttpt) REVERT: A 93 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8683 (pm20) REVERT: A 113 GLU cc_start: 0.9370 (tt0) cc_final: 0.8918 (tm-30) REVERT: A 201 HIS cc_start: 0.9338 (m90) cc_final: 0.8957 (m90) REVERT: A 206 GLN cc_start: 0.9446 (mm-40) cc_final: 0.9026 (mm110) REVERT: A 215 MET cc_start: 0.9466 (mmm) cc_final: 0.9117 (mmm) REVERT: A 246 LEU cc_start: 0.9701 (tp) cc_final: 0.9488 (tp) REVERT: A 250 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8580 (mm-30) REVERT: A 260 MET cc_start: 0.9644 (tpt) cc_final: 0.9406 (mmm) REVERT: A 282 GLU cc_start: 0.8829 (mp0) cc_final: 0.8538 (mp0) REVERT: A 300 LYS cc_start: 0.9248 (mttt) cc_final: 0.8768 (mppt) REVERT: A 301 LYS cc_start: 0.9310 (tptp) cc_final: 0.8984 (tptp) REVERT: A 305 ARG cc_start: 0.9039 (ptp-110) cc_final: 0.8815 (ptp-110) REVERT: A 343 PHE cc_start: 0.9658 (t80) cc_final: 0.9378 (t80) REVERT: A 403 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9011 (tp30) REVERT: A 410 MET cc_start: 0.8991 (tpt) cc_final: 0.8347 (tpp) REVERT: A 435 MET cc_start: 0.9025 (mmt) cc_final: 0.8764 (mmp) REVERT: A 454 MET cc_start: 0.9226 (mtt) cc_final: 0.8631 (tpp) REVERT: A 493 PHE cc_start: 0.9834 (t80) cc_final: 0.9129 (t80) REVERT: A 497 MET cc_start: 0.9336 (ttp) cc_final: 0.8810 (ttp) REVERT: A 526 TYR cc_start: 0.8746 (t80) cc_final: 0.8455 (t80) REVERT: A 537 PHE cc_start: 0.9586 (t80) cc_final: 0.8578 (t80) REVERT: A 554 MET cc_start: 0.9397 (ppp) cc_final: 0.8848 (ppp) REVERT: A 570 MET cc_start: 0.9471 (mmp) cc_final: 0.9071 (mmm) REVERT: A 580 ASP cc_start: 0.8806 (m-30) cc_final: 0.8356 (m-30) REVERT: A 605 GLU cc_start: 0.9370 (tt0) cc_final: 0.9081 (tt0) REVERT: B 57 ASP cc_start: 0.9227 (m-30) cc_final: 0.8903 (m-30) REVERT: B 70 CYS cc_start: 0.8462 (p) cc_final: 0.7914 (p) REVERT: B 99 MET cc_start: 0.9413 (mtp) cc_final: 0.8904 (tpp) REVERT: B 113 GLU cc_start: 0.9469 (tt0) cc_final: 0.8973 (tm-30) REVERT: B 118 GLN cc_start: 0.9525 (tt0) cc_final: 0.9184 (tm-30) REVERT: B 123 ILE cc_start: 0.9684 (mt) cc_final: 0.9351 (mt) REVERT: B 128 GLN cc_start: 0.9011 (pt0) cc_final: 0.8211 (tm-30) REVERT: B 181 LEU cc_start: 0.9726 (tp) cc_final: 0.9422 (pp) REVERT: B 182 LEU cc_start: 0.9805 (mm) cc_final: 0.9512 (mm) REVERT: B 209 LYS cc_start: 0.9075 (mttt) cc_final: 0.8535 (ttmm) REVERT: B 245 LYS cc_start: 0.9322 (mttt) cc_final: 0.8770 (ptpp) REVERT: B 260 MET cc_start: 0.9629 (mmm) cc_final: 0.9133 (mmm) REVERT: B 294 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8675 (mt-10) REVERT: B 297 ILE cc_start: 0.9536 (pt) cc_final: 0.9311 (tp) REVERT: B 300 LYS cc_start: 0.9118 (mttt) cc_final: 0.8575 (mppt) REVERT: B 306 GLN cc_start: 0.8792 (pt0) cc_final: 0.8520 (mp10) REVERT: B 343 PHE cc_start: 0.9704 (t80) cc_final: 0.9307 (t80) REVERT: B 347 CYS cc_start: 0.9067 (p) cc_final: 0.8692 (p) REVERT: B 403 GLU cc_start: 0.9162 (tp30) cc_final: 0.8827 (tp30) REVERT: B 421 LEU cc_start: 0.9421 (tp) cc_final: 0.8893 (tp) REVERT: B 454 MET cc_start: 0.9420 (mmt) cc_final: 0.8710 (tpp) REVERT: B 483 GLN cc_start: 0.9709 (tt0) cc_final: 0.9351 (tp40) REVERT: B 485 MET cc_start: 0.9642 (mmm) cc_final: 0.8630 (mmm) REVERT: B 497 MET cc_start: 0.9356 (ttp) cc_final: 0.8855 (ttp) REVERT: B 513 GLN cc_start: 0.9451 (tp-100) cc_final: 0.9069 (tp40) REVERT: B 528 MET cc_start: 0.8291 (mmp) cc_final: 0.7435 (mmm) REVERT: B 537 PHE cc_start: 0.9486 (t80) cc_final: 0.8280 (t80) REVERT: B 538 LEU cc_start: 0.9175 (mp) cc_final: 0.8960 (mp) REVERT: B 541 ILE cc_start: 0.8970 (pt) cc_final: 0.8686 (pt) REVERT: B 569 LEU cc_start: 0.9753 (tp) cc_final: 0.9543 (tp) REVERT: B 593 TRP cc_start: 0.9363 (t60) cc_final: 0.8870 (t60) REVERT: C 35 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9000 (mt-10) REVERT: C 93 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8882 (pm20) REVERT: C 96 MET cc_start: 0.9294 (mmt) cc_final: 0.8977 (mmp) REVERT: C 161 TYR cc_start: 0.8668 (t80) cc_final: 0.8442 (t80) REVERT: C 204 ILE cc_start: 0.9572 (mt) cc_final: 0.9325 (mt) REVERT: C 206 GLN cc_start: 0.9361 (mm-40) cc_final: 0.8788 (mm-40) REVERT: C 209 LYS cc_start: 0.8820 (mttt) cc_final: 0.8245 (ttmt) REVERT: C 215 MET cc_start: 0.9409 (mmp) cc_final: 0.9053 (mmm) REVERT: C 245 LYS cc_start: 0.9021 (mttt) cc_final: 0.8477 (ptpp) REVERT: C 246 LEU cc_start: 0.9615 (tp) cc_final: 0.9412 (tp) REVERT: C 260 MET cc_start: 0.9433 (mmp) cc_final: 0.8949 (mmp) REVERT: C 294 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8680 (mt-10) REVERT: C 300 LYS cc_start: 0.9204 (mttt) cc_final: 0.8730 (mppt) REVERT: C 301 LYS cc_start: 0.9444 (tptp) cc_final: 0.9038 (ttmt) REVERT: C 403 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8951 (tp30) REVERT: C 442 MET cc_start: 0.9665 (ttp) cc_final: 0.9439 (tmm) REVERT: C 454 MET cc_start: 0.9328 (mmt) cc_final: 0.8789 (tpp) REVERT: C 463 CYS cc_start: 0.9351 (m) cc_final: 0.9119 (m) REVERT: C 483 GLN cc_start: 0.9679 (tt0) cc_final: 0.9120 (mm-40) REVERT: C 485 MET cc_start: 0.9563 (mmm) cc_final: 0.8597 (mmm) REVERT: C 497 MET cc_start: 0.9237 (ttp) cc_final: 0.8766 (ttp) REVERT: C 518 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9047 (tm-30) REVERT: C 537 PHE cc_start: 0.9536 (t80) cc_final: 0.8804 (t80) REVERT: C 538 LEU cc_start: 0.9098 (mp) cc_final: 0.8886 (mp) REVERT: C 570 MET cc_start: 0.9476 (mmp) cc_final: 0.9207 (mmm) REVERT: C 593 TRP cc_start: 0.9280 (t60) cc_final: 0.9000 (t60) REVERT: D 35 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8794 (mt-10) REVERT: D 42 LYS cc_start: 0.9212 (tttt) cc_final: 0.8876 (pttm) REVERT: D 93 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8895 (pm20) REVERT: D 96 MET cc_start: 0.9418 (mmp) cc_final: 0.8965 (mmp) REVERT: D 99 MET cc_start: 0.9051 (mtm) cc_final: 0.8682 (ptp) REVERT: D 113 GLU cc_start: 0.9512 (tt0) cc_final: 0.9225 (tm-30) REVERT: D 204 ILE cc_start: 0.9572 (mt) cc_final: 0.9281 (mt) REVERT: D 206 GLN cc_start: 0.9403 (mm-40) cc_final: 0.8857 (mm-40) REVERT: D 209 LYS cc_start: 0.8508 (mttt) cc_final: 0.8159 (ttmt) REVERT: D 215 MET cc_start: 0.9458 (mmp) cc_final: 0.9096 (mmm) REVERT: D 245 LYS cc_start: 0.9056 (mttt) cc_final: 0.8512 (ptpp) REVERT: D 246 LEU cc_start: 0.9685 (tp) cc_final: 0.9440 (tp) REVERT: D 250 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8586 (mm-30) REVERT: D 260 MET cc_start: 0.9669 (tpt) cc_final: 0.9468 (mmm) REVERT: D 300 LYS cc_start: 0.9069 (mttt) cc_final: 0.8569 (mppt) REVERT: D 301 LYS cc_start: 0.9346 (tptp) cc_final: 0.8988 (tmtt) REVERT: D 403 GLU cc_start: 0.9419 (mm-30) cc_final: 0.8975 (tp30) REVERT: D 410 MET cc_start: 0.9207 (mmp) cc_final: 0.8957 (tpp) REVERT: D 421 LEU cc_start: 0.9499 (tp) cc_final: 0.9280 (tp) REVERT: D 440 MET cc_start: 0.8649 (mmm) cc_final: 0.8128 (mmm) REVERT: D 442 MET cc_start: 0.9738 (ttp) cc_final: 0.9360 (tmm) REVERT: D 445 ILE cc_start: 0.8541 (tp) cc_final: 0.8330 (tp) REVERT: D 463 CYS cc_start: 0.9194 (m) cc_final: 0.8987 (m) REVERT: D 483 GLN cc_start: 0.9752 (tt0) cc_final: 0.9365 (tp40) REVERT: D 485 MET cc_start: 0.9579 (mmm) cc_final: 0.9246 (tpp) REVERT: D 497 MET cc_start: 0.8775 (tmm) cc_final: 0.8273 (tmm) REVERT: D 511 ILE cc_start: 0.9847 (mt) cc_final: 0.9418 (mt) REVERT: D 570 MET cc_start: 0.9368 (mmp) cc_final: 0.9063 (mmm) REVERT: D 583 TRP cc_start: 0.8719 (p-90) cc_final: 0.8471 (p-90) REVERT: D 593 TRP cc_start: 0.9283 (t60) cc_final: 0.8773 (t60) REVERT: D 631 LEU cc_start: 0.9550 (tt) cc_final: 0.9297 (tt) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 0.2760 time to fit residues: 340.5641 Evaluate side-chains 662 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 201 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 84 HIS ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN A 464 ASN A 582 HIS B 582 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN D 483 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20602 Z= 0.193 Angle : 0.718 16.885 27945 Z= 0.350 Chirality : 0.044 0.187 3138 Planarity : 0.004 0.058 3522 Dihedral : 7.099 107.699 2798 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.17), residues: 2472 helix: -0.24 (0.14), residues: 1420 sheet: -3.94 (0.56), residues: 48 loop : -2.61 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 583 HIS 0.009 0.001 HIS B 84 PHE 0.019 0.001 PHE C 343 TYR 0.015 0.001 TYR C 526 ARG 0.007 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 774 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9567 (tp) cc_final: 0.9271 (tp) REVERT: A 42 LYS cc_start: 0.9435 (tttt) cc_final: 0.9057 (ttpt) REVERT: A 99 MET cc_start: 0.8386 (ttt) cc_final: 0.7656 (tmm) REVERT: A 113 GLU cc_start: 0.9377 (tt0) cc_final: 0.8932 (tm-30) REVERT: A 201 HIS cc_start: 0.9326 (m90) cc_final: 0.8951 (m90) REVERT: A 204 ILE cc_start: 0.9568 (mt) cc_final: 0.9325 (mt) REVERT: A 206 GLN cc_start: 0.9437 (mm-40) cc_final: 0.8913 (mm-40) REVERT: A 215 MET cc_start: 0.9468 (mmm) cc_final: 0.9095 (mmm) REVERT: A 246 LEU cc_start: 0.9694 (tp) cc_final: 0.9457 (tp) REVERT: A 250 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8613 (mm-30) REVERT: A 260 MET cc_start: 0.9651 (tpt) cc_final: 0.9414 (mmm) REVERT: A 300 LYS cc_start: 0.9262 (mttt) cc_final: 0.8801 (mppt) REVERT: A 301 LYS cc_start: 0.9253 (tptp) cc_final: 0.8908 (tptp) REVERT: A 305 ARG cc_start: 0.9073 (ptp-110) cc_final: 0.8814 (ptp-110) REVERT: A 343 PHE cc_start: 0.9660 (t80) cc_final: 0.9364 (t80) REVERT: A 403 GLU cc_start: 0.9429 (mm-30) cc_final: 0.9032 (tp30) REVERT: A 410 MET cc_start: 0.8999 (tpt) cc_final: 0.8367 (tpp) REVERT: A 421 LEU cc_start: 0.9331 (tp) cc_final: 0.9072 (tp) REVERT: A 435 MET cc_start: 0.9004 (mmt) cc_final: 0.8750 (mmp) REVERT: A 454 MET cc_start: 0.9244 (mtt) cc_final: 0.8652 (tpp) REVERT: A 483 GLN cc_start: 0.9733 (tt0) cc_final: 0.9134 (tp-100) REVERT: A 485 MET cc_start: 0.9677 (mmm) cc_final: 0.8731 (mmm) REVERT: A 493 PHE cc_start: 0.9836 (t80) cc_final: 0.9177 (t80) REVERT: A 497 MET cc_start: 0.9326 (ttp) cc_final: 0.8794 (ttp) REVERT: A 526 TYR cc_start: 0.8766 (t80) cc_final: 0.8558 (t80) REVERT: A 537 PHE cc_start: 0.9588 (t80) cc_final: 0.8559 (t80) REVERT: A 541 ILE cc_start: 0.8826 (pt) cc_final: 0.8444 (mm) REVERT: A 554 MET cc_start: 0.9413 (ppp) cc_final: 0.8854 (ppp) REVERT: A 570 MET cc_start: 0.9499 (mmp) cc_final: 0.9107 (mmm) REVERT: A 580 ASP cc_start: 0.8778 (m-30) cc_final: 0.8339 (m-30) REVERT: A 605 GLU cc_start: 0.9386 (tt0) cc_final: 0.9093 (tt0) REVERT: B 57 ASP cc_start: 0.9227 (m-30) cc_final: 0.8896 (m-30) REVERT: B 70 CYS cc_start: 0.8534 (p) cc_final: 0.8059 (p) REVERT: B 99 MET cc_start: 0.9461 (mtp) cc_final: 0.8897 (tpp) REVERT: B 113 GLU cc_start: 0.9465 (tt0) cc_final: 0.8962 (tm-30) REVERT: B 118 GLN cc_start: 0.9511 (tt0) cc_final: 0.9173 (tm-30) REVERT: B 123 ILE cc_start: 0.9682 (mt) cc_final: 0.9365 (mt) REVERT: B 181 LEU cc_start: 0.9726 (tp) cc_final: 0.9419 (pp) REVERT: B 182 LEU cc_start: 0.9806 (mm) cc_final: 0.9510 (mm) REVERT: B 206 GLN cc_start: 0.9601 (mm-40) cc_final: 0.8883 (mm110) REVERT: B 209 LYS cc_start: 0.9087 (mttt) cc_final: 0.8536 (ttmm) REVERT: B 245 LYS cc_start: 0.9311 (mttt) cc_final: 0.8769 (ptpp) REVERT: B 255 MET cc_start: 0.9553 (tpp) cc_final: 0.9345 (tpp) REVERT: B 260 MET cc_start: 0.9638 (mmm) cc_final: 0.9139 (mmm) REVERT: B 294 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 297 ILE cc_start: 0.9537 (pt) cc_final: 0.9318 (tp) REVERT: B 300 LYS cc_start: 0.9120 (mttt) cc_final: 0.8563 (mppt) REVERT: B 301 LYS cc_start: 0.9113 (tptp) cc_final: 0.8681 (tmtt) REVERT: B 306 GLN cc_start: 0.8874 (pt0) cc_final: 0.8440 (mp10) REVERT: B 323 ARG cc_start: 0.8778 (ptp-110) cc_final: 0.8564 (ptp-170) REVERT: B 343 PHE cc_start: 0.9705 (t80) cc_final: 0.9331 (t80) REVERT: B 347 CYS cc_start: 0.9071 (p) cc_final: 0.8677 (p) REVERT: B 400 LEU cc_start: 0.9629 (mt) cc_final: 0.9427 (mt) REVERT: B 421 LEU cc_start: 0.9440 (tp) cc_final: 0.8909 (tp) REVERT: B 442 MET cc_start: 0.9684 (ttp) cc_final: 0.9282 (tmm) REVERT: B 454 MET cc_start: 0.9407 (mmt) cc_final: 0.8702 (tpp) REVERT: B 483 GLN cc_start: 0.9708 (tt0) cc_final: 0.9146 (tp-100) REVERT: B 497 MET cc_start: 0.9269 (ttp) cc_final: 0.8838 (ttp) REVERT: B 513 GLN cc_start: 0.9482 (tp-100) cc_final: 0.9048 (tp40) REVERT: B 528 MET cc_start: 0.8276 (mmp) cc_final: 0.7419 (mmm) REVERT: B 537 PHE cc_start: 0.9488 (t80) cc_final: 0.8310 (t80) REVERT: B 538 LEU cc_start: 0.9171 (mp) cc_final: 0.8966 (mp) REVERT: B 541 ILE cc_start: 0.9034 (pt) cc_final: 0.8765 (pt) REVERT: B 577 MET cc_start: 0.9060 (ppp) cc_final: 0.8823 (ppp) REVERT: B 578 MET cc_start: 0.9449 (tpp) cc_final: 0.8958 (tpp) REVERT: B 593 TRP cc_start: 0.9354 (t60) cc_final: 0.8863 (t60) REVERT: B 631 LEU cc_start: 0.9511 (tt) cc_final: 0.9012 (tt) REVERT: C 35 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8968 (mt-10) REVERT: C 93 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8870 (pm20) REVERT: C 96 MET cc_start: 0.9306 (mmt) cc_final: 0.8990 (mmp) REVERT: C 161 TYR cc_start: 0.8705 (t80) cc_final: 0.8455 (t80) REVERT: C 204 ILE cc_start: 0.9578 (mt) cc_final: 0.9345 (mt) REVERT: C 206 GLN cc_start: 0.9373 (mm-40) cc_final: 0.8799 (mm-40) REVERT: C 209 LYS cc_start: 0.8820 (mttt) cc_final: 0.8257 (ttmt) REVERT: C 215 MET cc_start: 0.9434 (mmp) cc_final: 0.9143 (mmm) REVERT: C 245 LYS cc_start: 0.9017 (mttt) cc_final: 0.8484 (ptpp) REVERT: C 246 LEU cc_start: 0.9615 (tp) cc_final: 0.9410 (tp) REVERT: C 260 MET cc_start: 0.9412 (mmp) cc_final: 0.8954 (mmp) REVERT: C 294 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8689 (mt-10) REVERT: C 300 LYS cc_start: 0.9195 (mttt) cc_final: 0.8705 (mppt) REVERT: C 301 LYS cc_start: 0.9436 (tptp) cc_final: 0.9011 (ttmt) REVERT: C 403 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8971 (tp30) REVERT: C 442 MET cc_start: 0.9668 (ttp) cc_final: 0.9440 (tmm) REVERT: C 454 MET cc_start: 0.9333 (mmt) cc_final: 0.8703 (tpp) REVERT: C 463 CYS cc_start: 0.9351 (m) cc_final: 0.9125 (m) REVERT: C 483 GLN cc_start: 0.9685 (tt0) cc_final: 0.9180 (mm-40) REVERT: C 491 MET cc_start: 0.8541 (mtp) cc_final: 0.8277 (mtp) REVERT: C 497 MET cc_start: 0.9235 (ttp) cc_final: 0.8725 (ttp) REVERT: C 518 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9052 (tm-30) REVERT: C 537 PHE cc_start: 0.9529 (t80) cc_final: 0.8756 (t80) REVERT: C 538 LEU cc_start: 0.9100 (mp) cc_final: 0.8895 (mp) REVERT: C 570 MET cc_start: 0.9512 (mmp) cc_final: 0.9244 (mmm) REVERT: D 35 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8820 (mt-10) REVERT: D 42 LYS cc_start: 0.9215 (tttt) cc_final: 0.8877 (pttm) REVERT: D 93 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8839 (pm20) REVERT: D 96 MET cc_start: 0.9423 (mmp) cc_final: 0.8958 (mmm) REVERT: D 113 GLU cc_start: 0.9512 (tt0) cc_final: 0.9227 (tm-30) REVERT: D 204 ILE cc_start: 0.9566 (mt) cc_final: 0.9299 (mt) REVERT: D 206 GLN cc_start: 0.9414 (mm-40) cc_final: 0.8865 (mm-40) REVERT: D 209 LYS cc_start: 0.8764 (mttt) cc_final: 0.8181 (ttmt) REVERT: D 215 MET cc_start: 0.9466 (mmp) cc_final: 0.9083 (mmm) REVERT: D 245 LYS cc_start: 0.9054 (mttt) cc_final: 0.8514 (ptpp) REVERT: D 246 LEU cc_start: 0.9683 (tp) cc_final: 0.9441 (tp) REVERT: D 250 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8573 (mm-30) REVERT: D 300 LYS cc_start: 0.9165 (mttt) cc_final: 0.8669 (mppt) REVERT: D 301 LYS cc_start: 0.9351 (tptp) cc_final: 0.8995 (tmtt) REVERT: D 403 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8958 (tp30) REVERT: D 410 MET cc_start: 0.9191 (mmp) cc_final: 0.8950 (tpp) REVERT: D 421 LEU cc_start: 0.9500 (tp) cc_final: 0.9281 (tp) REVERT: D 440 MET cc_start: 0.8669 (mmm) cc_final: 0.8132 (mmm) REVERT: D 442 MET cc_start: 0.9746 (ttp) cc_final: 0.9489 (tmm) REVERT: D 483 GLN cc_start: 0.9719 (tt0) cc_final: 0.9312 (tp40) REVERT: D 485 MET cc_start: 0.9072 (mmm) cc_final: 0.8592 (tpp) REVERT: D 497 MET cc_start: 0.8844 (tmm) cc_final: 0.8320 (tmm) REVERT: D 570 MET cc_start: 0.9424 (mmp) cc_final: 0.9089 (mmm) REVERT: D 578 MET cc_start: 0.9390 (tpt) cc_final: 0.9159 (tpt) REVERT: D 583 TRP cc_start: 0.8701 (p-90) cc_final: 0.8440 (p-90) REVERT: D 593 TRP cc_start: 0.9288 (t60) cc_final: 0.8777 (t60) outliers start: 0 outliers final: 0 residues processed: 774 average time/residue: 0.2714 time to fit residues: 334.6378 Evaluate side-chains 668 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 chunk 227 optimal weight: 0.7980 chunk 196 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 151 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20602 Z= 0.186 Angle : 0.721 18.264 27945 Z= 0.350 Chirality : 0.044 0.164 3138 Planarity : 0.004 0.058 3522 Dihedral : 6.667 105.554 2798 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2472 helix: -0.21 (0.14), residues: 1424 sheet: -3.86 (0.56), residues: 48 loop : -2.57 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 583 HIS 0.010 0.001 HIS B 84 PHE 0.019 0.001 PHE C 343 TYR 0.015 0.001 TYR C 526 ARG 0.003 0.000 ARG A 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9555 (tp) cc_final: 0.9259 (tp) REVERT: A 42 LYS cc_start: 0.9430 (tttt) cc_final: 0.9050 (ttpt) REVERT: A 99 MET cc_start: 0.8410 (ttt) cc_final: 0.7656 (tmm) REVERT: A 113 GLU cc_start: 0.9371 (tt0) cc_final: 0.8913 (tm-30) REVERT: A 201 HIS cc_start: 0.9314 (m90) cc_final: 0.8959 (m90) REVERT: A 204 ILE cc_start: 0.9566 (mt) cc_final: 0.9291 (mt) REVERT: A 215 MET cc_start: 0.9469 (mmm) cc_final: 0.9082 (mmm) REVERT: A 246 LEU cc_start: 0.9689 (tp) cc_final: 0.9449 (tp) REVERT: A 250 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8605 (mm-30) REVERT: A 260 MET cc_start: 0.9651 (tpt) cc_final: 0.9413 (mmm) REVERT: A 300 LYS cc_start: 0.9259 (mttt) cc_final: 0.8812 (mppt) REVERT: A 301 LYS cc_start: 0.9224 (tptp) cc_final: 0.8876 (tptp) REVERT: A 305 ARG cc_start: 0.8961 (ptp-110) cc_final: 0.8663 (ptp-110) REVERT: A 336 TYR cc_start: 0.9320 (t80) cc_final: 0.8964 (t80) REVERT: A 343 PHE cc_start: 0.9661 (t80) cc_final: 0.9362 (t80) REVERT: A 403 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9015 (tp30) REVERT: A 410 MET cc_start: 0.9016 (tpt) cc_final: 0.8211 (tpp) REVERT: A 454 MET cc_start: 0.9262 (mtt) cc_final: 0.8634 (tpp) REVERT: A 463 CYS cc_start: 0.9499 (m) cc_final: 0.9219 (m) REVERT: A 493 PHE cc_start: 0.9838 (t80) cc_final: 0.9188 (t80) REVERT: A 497 MET cc_start: 0.9316 (ttp) cc_final: 0.8783 (ttp) REVERT: A 526 TYR cc_start: 0.8786 (t80) cc_final: 0.8583 (t80) REVERT: A 537 PHE cc_start: 0.9586 (t80) cc_final: 0.8533 (t80) REVERT: A 554 MET cc_start: 0.9419 (ppp) cc_final: 0.8870 (ppp) REVERT: A 580 ASP cc_start: 0.8608 (m-30) cc_final: 0.8225 (m-30) REVERT: A 603 MET cc_start: 0.9590 (ttp) cc_final: 0.8675 (tpp) REVERT: A 605 GLU cc_start: 0.9391 (tt0) cc_final: 0.9104 (tt0) REVERT: B 57 ASP cc_start: 0.9218 (m-30) cc_final: 0.8884 (m-30) REVERT: B 70 CYS cc_start: 0.8527 (p) cc_final: 0.8062 (p) REVERT: B 96 MET cc_start: 0.9646 (mmp) cc_final: 0.9383 (mmm) REVERT: B 99 MET cc_start: 0.9439 (mtp) cc_final: 0.8885 (tpp) REVERT: B 113 GLU cc_start: 0.9440 (tt0) cc_final: 0.8982 (tm-30) REVERT: B 181 LEU cc_start: 0.9703 (tp) cc_final: 0.9375 (pp) REVERT: B 182 LEU cc_start: 0.9805 (mm) cc_final: 0.9482 (mm) REVERT: B 206 GLN cc_start: 0.9588 (mm-40) cc_final: 0.8847 (mm110) REVERT: B 209 LYS cc_start: 0.9078 (mttt) cc_final: 0.8520 (ttmm) REVERT: B 245 LYS cc_start: 0.9305 (mttt) cc_final: 0.8749 (ptpp) REVERT: B 260 MET cc_start: 0.9641 (mmm) cc_final: 0.9134 (mmm) REVERT: B 294 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8661 (mt-10) REVERT: B 297 ILE cc_start: 0.9532 (pt) cc_final: 0.9331 (tp) REVERT: B 300 LYS cc_start: 0.9053 (mttt) cc_final: 0.8506 (mppt) REVERT: B 301 LYS cc_start: 0.9078 (tptp) cc_final: 0.8634 (tmtt) REVERT: B 343 PHE cc_start: 0.9706 (t80) cc_final: 0.9310 (t80) REVERT: B 347 CYS cc_start: 0.9083 (p) cc_final: 0.8703 (p) REVERT: B 406 ASP cc_start: 0.9276 (m-30) cc_final: 0.9003 (m-30) REVERT: B 421 LEU cc_start: 0.9444 (tp) cc_final: 0.8938 (tp) REVERT: B 442 MET cc_start: 0.9694 (ttp) cc_final: 0.9372 (tmm) REVERT: B 454 MET cc_start: 0.9399 (mmt) cc_final: 0.8675 (tpp) REVERT: B 483 GLN cc_start: 0.9718 (tt0) cc_final: 0.9165 (tp-100) REVERT: B 485 MET cc_start: 0.9732 (mmp) cc_final: 0.9476 (mmm) REVERT: B 497 MET cc_start: 0.9258 (ttp) cc_final: 0.8865 (ttp) REVERT: B 513 GLN cc_start: 0.9480 (tp-100) cc_final: 0.9038 (tp40) REVERT: B 528 MET cc_start: 0.8261 (mmp) cc_final: 0.7402 (mmm) REVERT: B 537 PHE cc_start: 0.9474 (t80) cc_final: 0.8310 (t80) REVERT: B 541 ILE cc_start: 0.9042 (pt) cc_final: 0.8788 (pt) REVERT: B 578 MET cc_start: 0.9545 (tpp) cc_final: 0.9325 (tpp) REVERT: B 593 TRP cc_start: 0.9329 (t60) cc_final: 0.8827 (t60) REVERT: B 631 LEU cc_start: 0.9483 (tt) cc_final: 0.9014 (tt) REVERT: C 35 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8928 (mt-10) REVERT: C 93 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8855 (pm20) REVERT: C 96 MET cc_start: 0.9309 (mmt) cc_final: 0.9002 (mmp) REVERT: C 161 TYR cc_start: 0.8706 (t80) cc_final: 0.8409 (t80) REVERT: C 204 ILE cc_start: 0.9587 (mt) cc_final: 0.9306 (mt) REVERT: C 209 LYS cc_start: 0.8838 (mttt) cc_final: 0.8228 (ttmt) REVERT: C 215 MET cc_start: 0.9437 (mmp) cc_final: 0.9145 (mmm) REVERT: C 245 LYS cc_start: 0.9000 (mttt) cc_final: 0.8457 (ptpp) REVERT: C 246 LEU cc_start: 0.9625 (tp) cc_final: 0.9407 (tp) REVERT: C 250 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8708 (mm-30) REVERT: C 260 MET cc_start: 0.9440 (mmp) cc_final: 0.8986 (mmp) REVERT: C 294 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8671 (mt-10) REVERT: C 300 LYS cc_start: 0.9211 (mttt) cc_final: 0.8673 (mppt) REVERT: C 301 LYS cc_start: 0.9441 (tptp) cc_final: 0.9025 (ttmt) REVERT: C 403 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9019 (tp30) REVERT: C 442 MET cc_start: 0.9669 (ttp) cc_final: 0.9444 (tmm) REVERT: C 454 MET cc_start: 0.9341 (mmt) cc_final: 0.8705 (tpp) REVERT: C 458 LEU cc_start: 0.9831 (mm) cc_final: 0.9631 (mm) REVERT: C 463 CYS cc_start: 0.9344 (m) cc_final: 0.9113 (m) REVERT: C 483 GLN cc_start: 0.9651 (tt0) cc_final: 0.9171 (mm-40) REVERT: C 497 MET cc_start: 0.9194 (ttp) cc_final: 0.8736 (ttp) REVERT: C 518 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9057 (tm-30) REVERT: C 537 PHE cc_start: 0.9530 (t80) cc_final: 0.8735 (t80) REVERT: C 538 LEU cc_start: 0.9111 (mp) cc_final: 0.8898 (mp) REVERT: D 35 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8817 (mt-10) REVERT: D 42 LYS cc_start: 0.9200 (tttt) cc_final: 0.8866 (pttm) REVERT: D 93 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8832 (pm20) REVERT: D 96 MET cc_start: 0.9397 (mmp) cc_final: 0.8950 (mmm) REVERT: D 113 GLU cc_start: 0.9525 (tt0) cc_final: 0.9231 (tm-30) REVERT: D 204 ILE cc_start: 0.9577 (mt) cc_final: 0.9303 (mt) REVERT: D 206 GLN cc_start: 0.9444 (mm-40) cc_final: 0.8917 (mm-40) REVERT: D 209 LYS cc_start: 0.8764 (mttt) cc_final: 0.8194 (ttmt) REVERT: D 215 MET cc_start: 0.9432 (mmp) cc_final: 0.9067 (mmm) REVERT: D 245 LYS cc_start: 0.9078 (mttt) cc_final: 0.8484 (ptpp) REVERT: D 246 LEU cc_start: 0.9674 (tp) cc_final: 0.9434 (tp) REVERT: D 250 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8635 (mm-30) REVERT: D 260 MET cc_start: 0.9389 (mmp) cc_final: 0.8933 (mmm) REVERT: D 300 LYS cc_start: 0.9231 (mttt) cc_final: 0.8723 (mppt) REVERT: D 301 LYS cc_start: 0.9353 (tptp) cc_final: 0.9000 (tmtt) REVERT: D 403 GLU cc_start: 0.9422 (mm-30) cc_final: 0.8954 (tp30) REVERT: D 406 ASP cc_start: 0.9379 (m-30) cc_final: 0.9020 (m-30) REVERT: D 410 MET cc_start: 0.9177 (mmp) cc_final: 0.8965 (tpp) REVERT: D 421 LEU cc_start: 0.9494 (tp) cc_final: 0.9276 (tp) REVERT: D 440 MET cc_start: 0.8670 (mmm) cc_final: 0.8123 (mmm) REVERT: D 442 MET cc_start: 0.9743 (ttp) cc_final: 0.9485 (tmm) REVERT: D 483 GLN cc_start: 0.9730 (tt0) cc_final: 0.9269 (tp40) REVERT: D 485 MET cc_start: 0.9110 (mmm) cc_final: 0.8570 (mmm) REVERT: D 497 MET cc_start: 0.8751 (tmm) cc_final: 0.8231 (tmm) REVERT: D 578 MET cc_start: 0.9380 (tpt) cc_final: 0.9167 (tpt) REVERT: D 583 TRP cc_start: 0.8695 (p-90) cc_final: 0.8416 (p-90) REVERT: D 593 TRP cc_start: 0.9280 (t60) cc_final: 0.8764 (t60) REVERT: D 605 GLU cc_start: 0.9215 (tt0) cc_final: 0.8988 (tt0) outliers start: 0 outliers final: 0 residues processed: 778 average time/residue: 0.2927 time to fit residues: 367.0047 Evaluate side-chains 660 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 24 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.056093 restraints weight = 64295.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.058926 restraints weight = 35641.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.061107 restraints weight = 23744.590| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20602 Z= 0.183 Angle : 0.708 9.827 27945 Z= 0.345 Chirality : 0.044 0.168 3138 Planarity : 0.004 0.057 3522 Dihedral : 6.470 96.252 2798 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2472 helix: -0.11 (0.14), residues: 1408 sheet: -3.83 (0.56), residues: 48 loop : -2.47 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 583 HIS 0.009 0.001 HIS B 84 PHE 0.019 0.001 PHE C 343 TYR 0.015 0.001 TYR C 526 ARG 0.003 0.000 ARG A 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6079.47 seconds wall clock time: 109 minutes 35.93 seconds (6575.93 seconds total)