Starting phenix.real_space_refine on Wed Aug 7 04:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oo4_20145/08_2024/6oo4_20145.cif" } resolution = 3.3 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= -0.000 sd= 0.011 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 98 5.16 5 C 12156 2.51 5 N 3116 2.21 5 O 3082 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 PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 367": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 682": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 367": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 682": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18452 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4561 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4573 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 226 Chain: "C" Number of atoms: 4561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4561 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 237 Chain: "D" Number of atoms: 4573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4573 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 23, 'TRANS': 586} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 8, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 18, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 226 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.28, per 1000 atoms: 0.56 Number of scatterers: 18452 At special positions: 0 Unit cell: (155.52, 156.6, 116.64, 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 98 16.00 O 3082 8.00 N 3116 7.00 C 12156 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 3.7 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 4 sheets defined 62.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 74 through 85 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.576A pdb=" N GLU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.668A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.666A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.899A pdb=" N VAL A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 259 through 280 Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.507A pdb=" N GLY A 287 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.557A pdb=" N GLY A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.542A pdb=" N PHE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'A' and resid 373 through 411 removed outlier: 4.506A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 428 through 457 Processing helix chain 'A' and resid 468 through 490 Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.202A pdb=" N LEU A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 516 removed outlier: 3.673A pdb=" N TYR A 513 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 514 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 515 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 516 " --> pdb=" O TYR A 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 516' Processing helix chain 'A' and resid 517 through 557 removed outlier: 4.145A pdb=" N TYR A 523 " --> pdb=" O HIS A 519 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.939A pdb=" N GLU A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 648 removed outlier: 3.786A pdb=" N VAL A 620 " --> pdb=" O PHE A 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 672 removed outlier: 4.410A pdb=" N TRP A 655 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.531A pdb=" N LEU B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.684A pdb=" N ASP B 89 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 133 through 145 removed outlier: 3.781A pdb=" N GLY B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.881A pdb=" N GLN B 198 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 220 through 230 removed outlier: 3.634A pdb=" N VAL B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.860A pdb=" N ALA B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 removed outlier: 3.763A pdb=" N SER B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 removed outlier: 3.710A pdb=" N ILE B 288 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.518A pdb=" N PHE B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 314 " --> pdb=" O LYS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 375 through 411 removed outlier: 3.733A pdb=" N LEU B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 428 through 457 Processing helix chain 'B' and resid 468 through 491 Processing helix chain 'B' and resid 494 through 509 removed outlier: 4.023A pdb=" N LEU B 498 " --> pdb=" O TRP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 516 removed outlier: 3.591A pdb=" N TYR B 513 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 514 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 515 " --> pdb=" O TYR B 512 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 516 " --> pdb=" O TYR B 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 516' Processing helix chain 'B' and resid 517 through 534 removed outlier: 4.377A pdb=" N TYR B 523 " --> pdb=" O HIS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 557 Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.784A pdb=" N GLU B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 648 removed outlier: 3.668A pdb=" N ASN B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 671 removed outlier: 4.271A pdb=" N TRP B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 133 through 145 removed outlier: 3.530A pdb=" N GLY C 145 " --> pdb=" O ASP C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.681A pdb=" N ILE C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.685A pdb=" N VAL C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.939A pdb=" N VAL C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 259 through 280 Processing helix chain 'C' and resid 284 through 288 removed outlier: 3.514A pdb=" N GLY C 287 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.541A pdb=" N GLY C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.542A pdb=" N PHE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN C 314 " --> pdb=" O LYS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 373 through 411 removed outlier: 4.501A pdb=" N LYS C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) Proline residue: C 389 - end of helix Processing helix chain 'C' and resid 428 through 457 Processing helix chain 'C' and resid 468 through 490 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.197A pdb=" N LEU C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 516 removed outlier: 3.676A pdb=" N TYR C 513 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 514 " --> pdb=" O LEU C 511 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 515 " --> pdb=" O TYR C 512 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 516 " --> pdb=" O TYR C 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 516' Processing helix chain 'C' and resid 517 through 557 removed outlier: 4.146A pdb=" N TYR C 523 " --> pdb=" O HIS C 519 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE C 538 " --> pdb=" O ASP C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.933A pdb=" N GLU C 597 " --> pdb=" O ASP C 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 603 " --> pdb=" O PHE C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 648 removed outlier: 3.787A pdb=" N VAL C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 672 removed outlier: 4.410A pdb=" N TRP C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 672 " --> pdb=" O GLU C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.747A pdb=" N LEU D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.711A pdb=" N ASP D 89 " --> pdb=" O ASN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 117 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.702A pdb=" N GLY D 145 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.876A pdb=" N GLN D 198 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'D' and resid 220 through 230 removed outlier: 3.600A pdb=" N VAL D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 255 removed outlier: 3.902A pdb=" N ALA D 255 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 280 removed outlier: 3.754A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.728A pdb=" N ILE D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.566A pdb=" N PHE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN D 314 " --> pdb=" O LYS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 373 through 411 removed outlier: 4.650A pdb=" N LYS D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 379 " --> pdb=" O PRO D 375 " (cutoff:3.500A) Proline residue: D 389 - end of helix Processing helix chain 'D' and resid 428 through 457 Processing helix chain 'D' and resid 468 through 491 Processing helix chain 'D' and resid 494 through 509 removed outlier: 4.033A pdb=" N LEU D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.589A pdb=" N TYR D 513 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 514 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY D 516 " --> pdb=" O TYR D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 510 through 516' Processing helix chain 'D' and resid 517 through 534 removed outlier: 4.379A pdb=" N TYR D 523 " --> pdb=" O HIS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 557 Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.796A pdb=" N GLU D 597 " --> pdb=" O ASP D 593 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 603 " --> pdb=" O PHE D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 648 removed outlier: 3.773A pdb=" N VAL D 620 " --> pdb=" O PHE D 616 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 671 removed outlier: 4.244A pdb=" N TRP D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN D 671 " --> pdb=" O LEU D 667 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 333 removed outlier: 6.845A pdb=" N VAL A 338 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N CYS A 332 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 336 " --> pdb=" O CYS A 332 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 690 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG A 700 " --> pdb=" O THR A 688 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 688 " --> pdb=" O ARG A 700 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS A 702 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET A 686 " --> pdb=" O CYS A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 327 through 333 removed outlier: 6.822A pdb=" N VAL B 338 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS B 332 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 336 " --> pdb=" O CYS B 332 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP B 698 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 327 through 333 removed outlier: 6.846A pdb=" N VAL C 338 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS C 332 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 336 " --> pdb=" O CYS C 332 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 690 " --> pdb=" O ASP C 698 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 700 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR C 688 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS C 702 " --> pdb=" O MET C 686 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N MET C 686 " --> pdb=" O CYS C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 327 through 333 removed outlier: 6.819A pdb=" N VAL D 338 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS D 332 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL D 336 " --> pdb=" O CYS D 332 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP D 698 " --> pdb=" O VAL D 689 " (cutoff:3.500A) 1070 hydrogen bonds defined for protein. 3180 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: 7.47 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2780 1.29 - 1.42: 5194 1.42 - 1.55: 10754 1.55 - 1.69: 42 1.69 - 1.82: 154 Bond restraints: 18924 Sorted by residual: bond pdb=" CAJ 6EU A1001 " pdb=" OAA 6EU A1001 " ideal model delta sigma weight residual 1.439 1.767 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" CAJ 6EU C1001 " pdb=" OAA 6EU C1001 " ideal model delta sigma weight residual 1.439 1.767 -0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" CAJ 6EU B1001 " pdb=" OAA 6EU B1001 " ideal model delta sigma weight residual 1.439 1.760 -0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" CAJ 6EU D1001 " pdb=" OAA 6EU D1001 " ideal model delta sigma weight residual 1.439 1.760 -0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" CAS 6EU D1001 " pdb=" CAX 6EU D1001 " ideal model delta sigma weight residual 1.334 1.588 -0.254 2.00e-02 2.50e+03 1.61e+02 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.67: 391 105.67 - 112.81: 10105 112.81 - 119.94: 6787 119.94 - 127.08: 8310 127.08 - 134.22: 289 Bond angle restraints: 25882 Sorted by residual: angle pdb=" N PRO C 413 " pdb=" CA PRO C 413 " pdb=" CB PRO C 413 " ideal model delta sigma weight residual 103.00 110.39 -7.39 1.10e+00 8.26e-01 4.51e+01 angle pdb=" N PRO B 413 " pdb=" CA PRO B 413 " pdb=" CB PRO B 413 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" N PRO D 413 " pdb=" CA PRO D 413 " pdb=" CB PRO D 413 " ideal model delta sigma weight residual 103.00 110.33 -7.33 1.10e+00 8.26e-01 4.44e+01 angle pdb=" N PRO A 413 " pdb=" CA PRO A 413 " pdb=" CB PRO A 413 " ideal model delta sigma weight residual 103.00 110.32 -7.32 1.10e+00 8.26e-01 4.43e+01 angle pdb=" CA GLN A 412 " pdb=" C GLN A 412 " pdb=" N PRO A 413 " ideal model delta sigma weight residual 120.58 116.82 3.76 7.40e-01 1.83e+00 2.58e+01 ... (remaining 25877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 10625 14.94 - 29.89: 498 29.89 - 44.83: 92 44.83 - 59.78: 33 59.78 - 74.72: 18 Dihedral angle restraints: 11266 sinusoidal: 4134 harmonic: 7132 Sorted by residual: dihedral pdb=" CA PHE C 207 " pdb=" C PHE C 207 " pdb=" N GLY C 208 " pdb=" CA GLY C 208 " ideal model delta harmonic sigma weight residual 180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE A 207 " pdb=" C PHE A 207 " pdb=" N GLY A 208 " pdb=" CA GLY A 208 " ideal model delta harmonic sigma weight residual -180.00 -153.28 -26.72 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER C 258 " pdb=" C SER C 258 " pdb=" N ALA C 259 " pdb=" CA ALA C 259 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2456 0.066 - 0.131: 498 0.131 - 0.197: 60 0.197 - 0.263: 8 0.263 - 0.329: 16 Chirality restraints: 3038 Sorted by residual: chirality pdb=" CAN 6EU A1001 " pdb=" CAJ 6EU A1001 " pdb=" CAP 6EU A1001 " pdb=" CAT 6EU A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.81 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CAL 6EU A1001 " pdb=" CAK 6EU A1001 " pdb=" CAM 6EU A1001 " pdb=" OAB 6EU A1001 " both_signs ideal model delta sigma weight residual False 2.77 2.44 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CAL 6EU C1001 " pdb=" CAK 6EU C1001 " pdb=" CAM 6EU C1001 " pdb=" OAB 6EU C1001 " both_signs ideal model delta sigma weight residual False 2.77 2.45 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 3035 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 405 " -0.022 2.00e-02 2.50e+03 2.02e-02 7.16e+00 pdb=" CG PHE A 405 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 405 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 405 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 405 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 405 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 405 " -0.022 2.00e-02 2.50e+03 1.99e-02 6.90e+00 pdb=" CG PHE B 405 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 405 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 405 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 405 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 405 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 405 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 405 " -0.021 2.00e-02 2.50e+03 1.97e-02 6.79e+00 pdb=" CG PHE C 405 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 405 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 405 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 405 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 405 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE C 405 " -0.003 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 12 2.47 - 3.07: 10992 3.07 - 3.68: 26556 3.68 - 4.29: 36796 4.29 - 4.90: 64338 Nonbonded interactions: 138694 Sorted by model distance: nonbonded pdb=" O ALA D 255 " pdb=" CE LYS D 305 " model vdw 1.858 3.440 nonbonded pdb=" O ALA C 255 " pdb=" CE LYS C 305 " model vdw 2.038 3.440 nonbonded pdb=" O ALA A 255 " pdb=" CE LYS A 305 " model vdw 2.047 3.440 nonbonded pdb=" O ALA B 255 " pdb=" CE LYS B 305 " model vdw 2.185 3.440 nonbonded pdb=" OG SER B 258 " pdb=" N ASN B 261 " model vdw 2.362 3.120 ... (remaining 138689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 93 or (resid 94 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 107 or (resid 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 156 or \ (resid 157 through 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 726 or resid 1001)) selection = (chain 'B' and (resid 73 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 237 or \ (resid 238 through 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 257 or (resid 258 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 302 or (resid \ 303 and (name N or name CA or name C or name O or name CB )) or resid 304 throug \ h 362 or (resid 363 through 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 726 or resid 1001)) selection = (chain 'C' and (resid 73 through 93 or (resid 94 through 95 and (name N or name \ CA or name C or name O or name CB )) or resid 96 through 107 or (resid 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 156 or \ (resid 157 through 158 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 175 or (resid 176 and (name N or name CA or name C or name \ O or name CB )) or resid 177 through 726 or resid 1001)) selection = (chain 'D' and (resid 73 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 216 or (resid 217 and \ (name N or name CA or name C or name O or name CB )) or resid 218 through 237 or \ (resid 238 through 239 and (name N or name CA or name C or name O or name CB )) \ or resid 240 through 257 or (resid 258 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 302 or (resid \ 303 and (name N or name CA or name C or name O or name CB )) or resid 304 throug \ h 362 or (resid 363 through 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 706 or (resid 707 and (name N or name CA or name C \ or name O or name CB )) or resid 708 through 726 or resid 1001)) } 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 individual isotropic 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: 1.160 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 53.070 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 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 : 0.013 0.328 18924 Z= 0.805 Angle : 1.103 14.028 25882 Z= 0.575 Chirality : 0.058 0.329 3038 Planarity : 0.007 0.061 3180 Dihedral : 10.408 74.723 6658 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.86 (0.13), residues: 2408 helix: -1.43 (0.11), residues: 1392 sheet: 0.89 (0.54), residues: 68 loop : -2.75 (0.14), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 713 HIS 0.011 0.003 HIS D 519 PHE 0.046 0.004 PHE A 405 TYR 0.031 0.004 TYR D 160 ARG 0.013 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.066 Fit side-chains REVERT: A 120 MET cc_start: 0.5498 (mtt) cc_final: 0.5264 (mtt) REVERT: A 133 CYS cc_start: 0.7196 (t) cc_final: 0.6850 (p) REVERT: A 195 HIS cc_start: 0.6219 (t-90) cc_final: 0.5620 (t70) REVERT: A 209 GLU cc_start: 0.6460 (mp0) cc_final: 0.6234 (mm-30) REVERT: A 221 TRP cc_start: 0.6425 (t-100) cc_final: 0.5955 (t-100) REVERT: A 225 ASN cc_start: 0.6552 (t0) cc_final: 0.6332 (m110) REVERT: A 270 ASP cc_start: 0.7713 (m-30) cc_final: 0.7459 (m-30) REVERT: A 337 ARG cc_start: 0.6385 (ptp-170) cc_final: 0.6182 (ptm160) REVERT: A 347 ASP cc_start: 0.7763 (t0) cc_final: 0.7314 (t0) REVERT: A 349 TRP cc_start: 0.7941 (t60) cc_final: 0.7741 (t60) REVERT: A 386 ARG cc_start: 0.7454 (ttt180) cc_final: 0.7143 (ttp80) REVERT: A 526 MET cc_start: 0.6395 (mmm) cc_final: 0.5917 (mtt) REVERT: A 613 GLN cc_start: 0.7683 (mt0) cc_final: 0.7413 (pm20) REVERT: A 692 ARG cc_start: 0.6945 (mtp180) cc_final: 0.5984 (mtm-85) REVERT: A 699 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 238 GLN cc_start: 0.8054 (mt0) cc_final: 0.7801 (mt0) REVERT: B 286 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7120 (mt-10) REVERT: B 381 GLN cc_start: 0.5893 (tp-100) cc_final: 0.5410 (tp-100) REVERT: B 452 TRP cc_start: 0.6584 (t60) cc_final: 0.6333 (t60) REVERT: B 455 TRP cc_start: 0.7607 (t-100) cc_final: 0.7056 (t-100) REVERT: B 526 MET cc_start: 0.6435 (mmm) cc_final: 0.6074 (mtt) REVERT: B 617 ARG cc_start: 0.7066 (ptt-90) cc_final: 0.6828 (ptt-90) REVERT: B 724 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6593 (mm-30) REVERT: C 120 MET cc_start: 0.5421 (mtt) cc_final: 0.5103 (mtt) REVERT: C 121 LYS cc_start: 0.7545 (tttp) cc_final: 0.7342 (tptp) REVERT: C 161 ARG cc_start: 0.5501 (ttt90) cc_final: 0.5249 (ttp80) REVERT: C 195 HIS cc_start: 0.6445 (t-90) cc_final: 0.5700 (t70) REVERT: C 232 HIS cc_start: 0.6501 (m90) cc_final: 0.6226 (m90) REVERT: C 270 ASP cc_start: 0.7522 (m-30) cc_final: 0.7194 (m-30) REVERT: C 347 ASP cc_start: 0.7476 (t0) cc_final: 0.7069 (t0) REVERT: C 386 ARG cc_start: 0.7268 (ttt180) cc_final: 0.6672 (mtt90) REVERT: C 526 MET cc_start: 0.6570 (mmm) cc_final: 0.6280 (mtt) REVERT: C 613 GLN cc_start: 0.7631 (mt0) cc_final: 0.7368 (pm20) REVERT: C 637 ASN cc_start: 0.7077 (t0) cc_final: 0.6875 (t0) REVERT: C 674 TRP cc_start: 0.8467 (p-90) cc_final: 0.8248 (p-90) REVERT: C 686 MET cc_start: 0.7738 (tmm) cc_final: 0.7526 (tmm) REVERT: C 692 ARG cc_start: 0.6833 (mtp180) cc_final: 0.5883 (mtt90) REVERT: C 699 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7106 (mt-10) REVERT: D 104 LEU cc_start: 0.6677 (mt) cc_final: 0.6350 (mp) REVERT: D 187 ASN cc_start: 0.6909 (t0) cc_final: 0.6613 (t0) REVERT: D 236 SER cc_start: 0.7807 (t) cc_final: 0.7365 (p) REVERT: D 452 TRP cc_start: 0.6693 (t60) cc_final: 0.6244 (t60) REVERT: D 455 TRP cc_start: 0.7302 (t-100) cc_final: 0.6766 (t-100) REVERT: D 526 MET cc_start: 0.6515 (mmm) cc_final: 0.6175 (mtt) REVERT: D 709 ASN cc_start: 0.7851 (t0) cc_final: 0.7603 (t0) REVERT: D 724 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6576 (mm-30) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3562 time to fit residues: 146.7888 Evaluate side-chains 192 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 98 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN C 225 ASN D 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18924 Z= 0.181 Angle : 0.571 8.414 25882 Z= 0.287 Chirality : 0.037 0.189 3038 Planarity : 0.004 0.045 3180 Dihedral : 6.210 58.402 3000 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.47 % Allowed : 4.88 % Favored : 94.65 % 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: -0.19 (0.16), residues: 2408 helix: 1.02 (0.13), residues: 1420 sheet: 1.03 (0.54), residues: 68 loop : -2.13 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 507 HIS 0.004 0.001 HIS C 519 PHE 0.018 0.001 PHE A 309 TYR 0.012 0.001 TYR D 206 ARG 0.005 0.000 ARG D 615 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.4838 (m110) cc_final: 0.4623 (m110) REVERT: A 195 HIS cc_start: 0.6090 (t-90) cc_final: 0.5818 (t70) REVERT: A 221 TRP cc_start: 0.6401 (t-100) cc_final: 0.5728 (t-100) REVERT: A 270 ASP cc_start: 0.7680 (m-30) cc_final: 0.7423 (m-30) REVERT: A 347 ASP cc_start: 0.7879 (t0) cc_final: 0.7430 (t0) REVERT: A 349 TRP cc_start: 0.7830 (t60) cc_final: 0.7494 (t60) REVERT: A 386 ARG cc_start: 0.7313 (ttt180) cc_final: 0.7042 (ttp80) REVERT: A 692 ARG cc_start: 0.6942 (mtp180) cc_final: 0.6046 (mtt90) REVERT: A 699 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7356 (mt-10) REVERT: B 121 LYS cc_start: 0.6742 (tptm) cc_final: 0.6391 (tptt) REVERT: B 238 GLN cc_start: 0.8038 (mt0) cc_final: 0.7640 (mt0) REVERT: B 526 MET cc_start: 0.6346 (mmm) cc_final: 0.5943 (mtt) REVERT: B 724 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6613 (mm-30) REVERT: C 135 GLN cc_start: 0.6955 (tt0) cc_final: 0.6561 (tp40) REVERT: C 195 HIS cc_start: 0.6107 (t-90) cc_final: 0.5387 (t70) REVERT: C 232 HIS cc_start: 0.6487 (m90) cc_final: 0.6171 (m90) REVERT: C 270 ASP cc_start: 0.7566 (m-30) cc_final: 0.7259 (m-30) REVERT: C 347 ASP cc_start: 0.7670 (t0) cc_final: 0.7239 (t0) REVERT: C 386 ARG cc_start: 0.7162 (ttt180) cc_final: 0.6620 (mtt90) REVERT: C 526 MET cc_start: 0.6641 (mmm) cc_final: 0.6243 (mtt) REVERT: C 637 ASN cc_start: 0.6943 (t0) cc_final: 0.6678 (t0) REVERT: C 674 TRP cc_start: 0.8457 (p-90) cc_final: 0.8248 (p-90) REVERT: C 692 ARG cc_start: 0.6840 (mtp180) cc_final: 0.5881 (mtt90) REVERT: C 699 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 121 LYS cc_start: 0.6765 (tptt) cc_final: 0.6544 (tptt) REVERT: D 187 ASN cc_start: 0.6854 (t0) cc_final: 0.6497 (t0) REVERT: D 236 SER cc_start: 0.7945 (t) cc_final: 0.7478 (p) REVERT: D 452 TRP cc_start: 0.6446 (t60) cc_final: 0.6053 (t60) REVERT: D 526 MET cc_start: 0.6534 (mmm) cc_final: 0.6149 (mtt) REVERT: D 699 GLU cc_start: 0.7540 (tt0) cc_final: 0.7315 (tm-30) REVERT: D 724 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6683 (mm-30) outliers start: 8 outliers final: 7 residues processed: 217 average time/residue: 0.2836 time to fit residues: 96.2231 Evaluate side-chains 187 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 555 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 0.6980 chunk 239 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 485 GLN B 232 HIS C 485 GLN D 232 HIS D 436 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 18924 Z= 0.508 Angle : 0.745 10.139 25882 Z= 0.371 Chirality : 0.045 0.183 3038 Planarity : 0.005 0.043 3180 Dihedral : 6.651 86.842 3000 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.47 % Allowed : 7.05 % Favored : 91.48 % 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: 0.21 (0.16), residues: 2408 helix: 1.35 (0.14), residues: 1420 sheet: 1.33 (0.60), residues: 68 loop : -1.99 (0.17), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 713 HIS 0.010 0.002 HIS D 519 PHE 0.037 0.003 PHE B 405 TYR 0.021 0.003 TYR B 401 ARG 0.005 0.001 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7599 (m-30) cc_final: 0.7324 (m-30) REVERT: A 347 ASP cc_start: 0.7974 (t0) cc_final: 0.7435 (t0) REVERT: A 386 ARG cc_start: 0.7295 (ttt180) cc_final: 0.6967 (ttp80) REVERT: A 692 ARG cc_start: 0.7027 (mtp180) cc_final: 0.6060 (mtt90) REVERT: A 699 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 121 LYS cc_start: 0.6381 (tptm) cc_final: 0.5991 (tptt) REVERT: B 238 GLN cc_start: 0.8170 (mt0) cc_final: 0.7907 (mt0) REVERT: B 526 MET cc_start: 0.6410 (mmm) cc_final: 0.5950 (mtt) REVERT: B 724 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6553 (mm-30) REVERT: C 195 HIS cc_start: 0.6299 (t-90) cc_final: 0.5602 (t70) REVERT: C 232 HIS cc_start: 0.6438 (m90) cc_final: 0.6161 (m90) REVERT: C 270 ASP cc_start: 0.7535 (m-30) cc_final: 0.7269 (m-30) REVERT: C 347 ASP cc_start: 0.7839 (t0) cc_final: 0.7336 (t0) REVERT: C 386 ARG cc_start: 0.7316 (ttt180) cc_final: 0.6982 (ttp80) REVERT: C 526 MET cc_start: 0.6495 (mmm) cc_final: 0.6019 (mtt) REVERT: C 637 ASN cc_start: 0.7120 (t0) cc_final: 0.6832 (t0) REVERT: C 692 ARG cc_start: 0.6989 (mtp180) cc_final: 0.5949 (mtm-85) REVERT: C 699 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7224 (mt-10) REVERT: D 121 LYS cc_start: 0.6633 (tptt) cc_final: 0.6387 (tptt) REVERT: D 452 TRP cc_start: 0.6390 (t60) cc_final: 0.5862 (t60) REVERT: D 526 MET cc_start: 0.6546 (mmm) cc_final: 0.6086 (mtt) REVERT: D 708 MET cc_start: 0.7368 (tpp) cc_final: 0.7163 (tpp) REVERT: D 724 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6635 (mm-30) outliers start: 25 outliers final: 15 residues processed: 188 average time/residue: 0.3000 time to fit residues: 87.6783 Evaluate side-chains 183 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 168 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 555 SER Chi-restraints excluded: chain D residue 644 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.0070 chunk 222 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18924 Z= 0.140 Angle : 0.513 8.798 25882 Z= 0.255 Chirality : 0.036 0.161 3038 Planarity : 0.003 0.042 3180 Dihedral : 5.617 55.635 3000 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.12 % Allowed : 8.34 % Favored : 90.54 % 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: 1.20 (0.17), residues: 2408 helix: 2.16 (0.14), residues: 1436 sheet: 1.30 (0.60), residues: 68 loop : -1.62 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 452 HIS 0.003 0.001 HIS C 249 PHE 0.015 0.001 PHE A 309 TYR 0.011 0.001 TYR C 469 ARG 0.003 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7599 (m-30) cc_final: 0.7348 (m-30) REVERT: A 316 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7263 (mt-10) REVERT: A 347 ASP cc_start: 0.7776 (t0) cc_final: 0.7361 (t0) REVERT: A 386 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6877 (ttp80) REVERT: A 514 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7566 (p) REVERT: A 692 ARG cc_start: 0.7011 (mtp180) cc_final: 0.5970 (mtm-85) REVERT: A 699 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7256 (mt-10) REVERT: B 121 LYS cc_start: 0.6588 (tptm) cc_final: 0.6135 (tptt) REVERT: B 238 GLN cc_start: 0.8110 (mt0) cc_final: 0.7859 (mt0) REVERT: B 402 MET cc_start: 0.6907 (mmt) cc_final: 0.6581 (mmp) REVERT: B 526 MET cc_start: 0.6349 (mmm) cc_final: 0.5875 (mtt) REVERT: B 670 GLU cc_start: 0.7123 (tt0) cc_final: 0.6778 (tt0) REVERT: B 724 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6691 (mm-30) REVERT: C 135 GLN cc_start: 0.7229 (tt0) cc_final: 0.6895 (tp40) REVERT: C 195 HIS cc_start: 0.5910 (t-90) cc_final: 0.5224 (t70) REVERT: C 232 HIS cc_start: 0.6428 (m90) cc_final: 0.6135 (m90) REVERT: C 243 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6345 (tt) REVERT: C 270 ASP cc_start: 0.7467 (m-30) cc_final: 0.7170 (m-30) REVERT: C 347 ASP cc_start: 0.7782 (t0) cc_final: 0.7380 (t0) REVERT: C 386 ARG cc_start: 0.7218 (ttt180) cc_final: 0.6915 (ttp80) REVERT: C 452 TRP cc_start: 0.5654 (t60) cc_final: 0.5049 (t60) REVERT: C 469 TYR cc_start: 0.6706 (t80) cc_final: 0.6480 (t80) REVERT: C 514 THR cc_start: 0.7777 (OUTLIER) cc_final: 0.7519 (p) REVERT: C 692 ARG cc_start: 0.6965 (mtp180) cc_final: 0.5924 (mtm-85) REVERT: C 699 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7306 (mt-10) REVERT: D 452 TRP cc_start: 0.6465 (t60) cc_final: 0.5957 (t60) REVERT: D 526 MET cc_start: 0.6356 (mmm) cc_final: 0.5889 (mtt) REVERT: D 687 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5395 (pp) REVERT: D 724 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6636 (mm-30) outliers start: 19 outliers final: 7 residues processed: 214 average time/residue: 0.2804 time to fit residues: 93.3823 Evaluate side-chains 190 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18924 Z= 0.190 Angle : 0.522 8.762 25882 Z= 0.258 Chirality : 0.036 0.152 3038 Planarity : 0.003 0.040 3180 Dihedral : 5.517 57.967 3000 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.29 % Allowed : 9.87 % Favored : 88.84 % 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: 1.44 (0.17), residues: 2408 helix: 2.42 (0.14), residues: 1428 sheet: 1.21 (0.59), residues: 68 loop : -1.58 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 452 HIS 0.004 0.001 HIS D 519 PHE 0.015 0.001 PHE C 309 TYR 0.012 0.001 TYR D 206 ARG 0.003 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7037 (tppt) cc_final: 0.6804 (tptt) REVERT: A 270 ASP cc_start: 0.7661 (m-30) cc_final: 0.7364 (m-30) REVERT: A 316 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7263 (mt-10) REVERT: A 347 ASP cc_start: 0.7964 (t0) cc_final: 0.7528 (t0) REVERT: A 386 ARG cc_start: 0.7288 (ttt180) cc_final: 0.7004 (ttp80) REVERT: A 514 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7583 (p) REVERT: A 692 ARG cc_start: 0.7084 (mtp180) cc_final: 0.6046 (mtm-85) REVERT: A 699 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7379 (mt-10) REVERT: B 121 LYS cc_start: 0.6584 (tptm) cc_final: 0.6135 (tptt) REVERT: B 236 SER cc_start: 0.7950 (t) cc_final: 0.7496 (p) REVERT: B 238 GLN cc_start: 0.8111 (mt0) cc_final: 0.7903 (mt0) REVERT: B 402 MET cc_start: 0.6904 (mmt) cc_final: 0.6579 (mmp) REVERT: B 526 MET cc_start: 0.6329 (mmm) cc_final: 0.5850 (mtt) REVERT: B 670 GLU cc_start: 0.7105 (tt0) cc_final: 0.6769 (tt0) REVERT: B 687 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5332 (pp) REVERT: B 724 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6694 (mm-30) REVERT: C 135 GLN cc_start: 0.7214 (tt0) cc_final: 0.6878 (tp40) REVERT: C 195 HIS cc_start: 0.6168 (t-90) cc_final: 0.5450 (t70) REVERT: C 232 HIS cc_start: 0.6442 (m90) cc_final: 0.6192 (m90) REVERT: C 243 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6355 (tt) REVERT: C 270 ASP cc_start: 0.7481 (m-30) cc_final: 0.7183 (m-30) REVERT: C 347 ASP cc_start: 0.7836 (t0) cc_final: 0.7446 (t0) REVERT: C 386 ARG cc_start: 0.7219 (ttt180) cc_final: 0.6927 (ttp80) REVERT: C 469 TYR cc_start: 0.6832 (t80) cc_final: 0.6494 (t80) REVERT: C 514 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7533 (p) REVERT: C 692 ARG cc_start: 0.7004 (mtp180) cc_final: 0.5950 (mtm-85) REVERT: C 699 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7243 (mt-10) REVERT: D 526 MET cc_start: 0.6388 (mmm) cc_final: 0.5917 (mtt) REVERT: D 687 LEU cc_start: 0.5914 (OUTLIER) cc_final: 0.5402 (pp) REVERT: D 724 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6557 (mm-30) outliers start: 22 outliers final: 13 residues processed: 199 average time/residue: 0.2761 time to fit residues: 86.6520 Evaluate side-chains 195 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 0.5980 chunk 212 optimal weight: 0.0470 chunk 46 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 637 ASN D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6079 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18924 Z= 0.129 Angle : 0.477 8.501 25882 Z= 0.235 Chirality : 0.035 0.149 3038 Planarity : 0.003 0.040 3180 Dihedral : 5.203 60.733 3000 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.29 % Allowed : 10.28 % Favored : 88.43 % 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: 1.81 (0.17), residues: 2408 helix: 2.69 (0.14), residues: 1440 sheet: 1.18 (0.58), residues: 68 loop : -1.44 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 452 HIS 0.002 0.000 HIS A 519 PHE 0.013 0.001 PHE C 309 TYR 0.012 0.001 TYR B 523 ARG 0.002 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7082 (tppt) cc_final: 0.6853 (tptt) REVERT: A 270 ASP cc_start: 0.7655 (m-30) cc_final: 0.7390 (m-30) REVERT: A 316 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 347 ASP cc_start: 0.7862 (t0) cc_final: 0.7446 (t0) REVERT: A 386 ARG cc_start: 0.7263 (ttt180) cc_final: 0.6978 (ttp80) REVERT: A 514 THR cc_start: 0.7754 (OUTLIER) cc_final: 0.7492 (p) REVERT: A 692 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6026 (mtm-85) REVERT: A 699 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 121 LYS cc_start: 0.6650 (tptm) cc_final: 0.6211 (tptt) REVERT: B 236 SER cc_start: 0.7876 (t) cc_final: 0.7461 (p) REVERT: B 526 MET cc_start: 0.6459 (mmm) cc_final: 0.5996 (mtt) REVERT: B 670 GLU cc_start: 0.6733 (tt0) cc_final: 0.6442 (tt0) REVERT: B 687 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5329 (pp) REVERT: B 699 GLU cc_start: 0.7473 (pt0) cc_final: 0.7002 (tt0) REVERT: B 724 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6730 (mm-30) REVERT: C 135 GLN cc_start: 0.7386 (tt0) cc_final: 0.7052 (tp40) REVERT: C 195 HIS cc_start: 0.5951 (t-90) cc_final: 0.5705 (t70) REVERT: C 232 HIS cc_start: 0.6374 (m90) cc_final: 0.6135 (m90) REVERT: C 243 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6271 (tt) REVERT: C 270 ASP cc_start: 0.7476 (m-30) cc_final: 0.7162 (m-30) REVERT: C 316 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 347 ASP cc_start: 0.7763 (t0) cc_final: 0.7378 (t0) REVERT: C 386 ARG cc_start: 0.7129 (ttt180) cc_final: 0.6860 (ttp80) REVERT: C 452 TRP cc_start: 0.5630 (t60) cc_final: 0.5193 (t60) REVERT: C 514 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7474 (p) REVERT: C 692 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6036 (mtm-85) REVERT: C 699 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7216 (mt-10) REVERT: D 452 TRP cc_start: 0.6531 (t60) cc_final: 0.6094 (t60) REVERT: D 526 MET cc_start: 0.6352 (mmm) cc_final: 0.5874 (mtt) REVERT: D 687 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5396 (pp) REVERT: D 724 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6514 (mm-30) outliers start: 22 outliers final: 9 residues processed: 220 average time/residue: 0.3017 time to fit residues: 104.1085 Evaluate side-chains 204 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6097 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18924 Z= 0.164 Angle : 0.499 8.272 25882 Z= 0.245 Chirality : 0.036 0.165 3038 Planarity : 0.003 0.040 3180 Dihedral : 5.242 64.805 3000 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.53 % Allowed : 11.16 % Favored : 87.31 % 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: 1.87 (0.17), residues: 2408 helix: 2.74 (0.14), residues: 1440 sheet: 1.17 (0.58), residues: 68 loop : -1.41 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 452 HIS 0.003 0.001 HIS D 519 PHE 0.013 0.001 PHE C 309 TYR 0.021 0.001 TYR A 445 ARG 0.007 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7664 (m-30) cc_final: 0.7353 (m-30) REVERT: A 316 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 347 ASP cc_start: 0.7963 (t0) cc_final: 0.7531 (t0) REVERT: A 386 ARG cc_start: 0.7287 (ttt180) cc_final: 0.7001 (ttp80) REVERT: A 514 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 692 ARG cc_start: 0.7090 (mtp180) cc_final: 0.6046 (mtm-85) REVERT: A 699 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 236 SER cc_start: 0.7893 (t) cc_final: 0.7477 (p) REVERT: B 526 MET cc_start: 0.6300 (mmm) cc_final: 0.5841 (mtt) REVERT: B 670 GLU cc_start: 0.6787 (tt0) cc_final: 0.6486 (tt0) REVERT: B 687 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5342 (pp) REVERT: B 699 GLU cc_start: 0.7473 (pt0) cc_final: 0.7007 (tt0) REVERT: B 724 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6731 (mm-30) REVERT: C 135 GLN cc_start: 0.7376 (tt0) cc_final: 0.7057 (tp40) REVERT: C 184 ASN cc_start: 0.5801 (m110) cc_final: 0.5428 (m110) REVERT: C 195 HIS cc_start: 0.6061 (t-90) cc_final: 0.5832 (t70) REVERT: C 232 HIS cc_start: 0.6396 (m90) cc_final: 0.6163 (m90) REVERT: C 243 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6332 (tt) REVERT: C 270 ASP cc_start: 0.7483 (m-30) cc_final: 0.7172 (m-30) REVERT: C 316 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 347 ASP cc_start: 0.7867 (t0) cc_final: 0.7445 (t0) REVERT: C 386 ARG cc_start: 0.7139 (ttt180) cc_final: 0.6869 (ttp80) REVERT: C 514 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7641 (t) REVERT: C 692 ARG cc_start: 0.6980 (mtp180) cc_final: 0.5856 (mtm-85) REVERT: C 699 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7238 (mt-10) REVERT: D 452 TRP cc_start: 0.6543 (t60) cc_final: 0.6099 (t60) REVERT: D 514 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7684 (p) REVERT: D 526 MET cc_start: 0.6365 (mmm) cc_final: 0.5879 (mtt) REVERT: D 687 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5296 (pp) REVERT: D 724 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6544 (mm-30) outliers start: 26 outliers final: 15 residues processed: 210 average time/residue: 0.2874 time to fit residues: 95.1393 Evaluate side-chains 207 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 149 optimal weight: 0.0060 chunk 160 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18924 Z= 0.132 Angle : 0.488 8.211 25882 Z= 0.240 Chirality : 0.035 0.159 3038 Planarity : 0.003 0.040 3180 Dihedral : 5.144 71.384 3000 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 11.22 % Favored : 87.54 % 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: 2.02 (0.17), residues: 2408 helix: 2.89 (0.14), residues: 1436 sheet: 1.19 (0.58), residues: 68 loop : -1.37 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 674 HIS 0.003 0.001 HIS D 519 PHE 0.012 0.001 PHE C 309 TYR 0.019 0.001 TYR A 445 ARG 0.006 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7655 (m-30) cc_final: 0.7390 (m-30) REVERT: A 316 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7237 (mt-10) REVERT: A 347 ASP cc_start: 0.7940 (t0) cc_final: 0.7520 (t0) REVERT: A 386 ARG cc_start: 0.7275 (ttt180) cc_final: 0.6992 (ttp80) REVERT: A 514 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7463 (p) REVERT: A 692 ARG cc_start: 0.7133 (mtp180) cc_final: 0.6056 (mtm-85) REVERT: A 699 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7447 (mt-10) REVERT: B 121 LYS cc_start: 0.6702 (tptm) cc_final: 0.6250 (tptt) REVERT: B 236 SER cc_start: 0.7893 (t) cc_final: 0.7477 (p) REVERT: B 526 MET cc_start: 0.6296 (mmm) cc_final: 0.5828 (mtt) REVERT: B 670 GLU cc_start: 0.6713 (tt0) cc_final: 0.6436 (tt0) REVERT: B 687 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5326 (pp) REVERT: B 699 GLU cc_start: 0.7483 (pt0) cc_final: 0.7038 (tt0) REVERT: B 724 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6736 (mm-30) REVERT: C 125 ASN cc_start: 0.5071 (m110) cc_final: 0.4833 (m110) REVERT: C 135 GLN cc_start: 0.7370 (tt0) cc_final: 0.7044 (tp40) REVERT: C 195 HIS cc_start: 0.6000 (t-90) cc_final: 0.5798 (t70) REVERT: C 232 HIS cc_start: 0.6408 (m90) cc_final: 0.6175 (m90) REVERT: C 243 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6318 (tt) REVERT: C 270 ASP cc_start: 0.7480 (m-30) cc_final: 0.7164 (m-30) REVERT: C 316 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7430 (mt-10) REVERT: C 347 ASP cc_start: 0.7871 (t0) cc_final: 0.7471 (t0) REVERT: C 386 ARG cc_start: 0.7106 (ttt180) cc_final: 0.6835 (ttp80) REVERT: C 452 TRP cc_start: 0.5622 (t60) cc_final: 0.5199 (t60) REVERT: C 514 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7458 (p) REVERT: C 692 ARG cc_start: 0.6982 (mtp180) cc_final: 0.5863 (mtm-85) REVERT: C 699 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7239 (mt-10) REVERT: D 452 TRP cc_start: 0.6428 (t60) cc_final: 0.5942 (t60) REVERT: D 514 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7581 (p) REVERT: D 526 MET cc_start: 0.6368 (mmm) cc_final: 0.5871 (mtt) REVERT: D 687 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5452 (pp) REVERT: D 724 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6568 (mm-30) outliers start: 21 outliers final: 14 residues processed: 208 average time/residue: 0.2637 time to fit residues: 87.1237 Evaluate side-chains 211 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.7980 chunk 225 optimal weight: 0.0970 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 172 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 218 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 637 ASN D 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18924 Z= 0.129 Angle : 0.481 8.000 25882 Z= 0.235 Chirality : 0.035 0.163 3038 Planarity : 0.003 0.040 3180 Dihedral : 5.021 75.434 3000 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 10.87 % Favored : 87.60 % 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: 2.15 (0.17), residues: 2408 helix: 2.98 (0.13), residues: 1436 sheet: 1.23 (0.58), residues: 68 loop : -1.29 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 674 HIS 0.002 0.001 HIS D 519 PHE 0.011 0.001 PHE C 309 TYR 0.018 0.001 TYR A 445 ARG 0.006 0.000 ARG B 615 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 ASP cc_start: 0.7704 (m-30) cc_final: 0.7446 (m-30) REVERT: A 316 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 347 ASP cc_start: 0.7914 (t0) cc_final: 0.7556 (t70) REVERT: A 386 ARG cc_start: 0.7249 (ttt180) cc_final: 0.6964 (ttp80) REVERT: A 514 THR cc_start: 0.7750 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 692 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6037 (mtm-85) REVERT: A 699 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 121 LYS cc_start: 0.6751 (tptm) cc_final: 0.6319 (tptt) REVERT: B 236 SER cc_start: 0.7892 (t) cc_final: 0.7475 (p) REVERT: B 514 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7617 (p) REVERT: B 526 MET cc_start: 0.6315 (mmm) cc_final: 0.5834 (mtt) REVERT: B 670 GLU cc_start: 0.6694 (tt0) cc_final: 0.6403 (tt0) REVERT: B 687 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5324 (pp) REVERT: B 699 GLU cc_start: 0.7485 (pt0) cc_final: 0.7037 (tt0) REVERT: B 724 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6834 (mm-30) REVERT: C 135 GLN cc_start: 0.7391 (tt0) cc_final: 0.7096 (tp40) REVERT: C 184 ASN cc_start: 0.5863 (m110) cc_final: 0.5493 (m110) REVERT: C 195 HIS cc_start: 0.6047 (t-90) cc_final: 0.5843 (t70) REVERT: C 232 HIS cc_start: 0.6411 (m90) cc_final: 0.6173 (m90) REVERT: C 243 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6287 (tt) REVERT: C 270 ASP cc_start: 0.7563 (m-30) cc_final: 0.7246 (m-30) REVERT: C 316 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 347 ASP cc_start: 0.7925 (t0) cc_final: 0.7519 (t0) REVERT: C 386 ARG cc_start: 0.7110 (ttt180) cc_final: 0.6807 (ttp80) REVERT: C 402 MET cc_start: 0.6375 (mmt) cc_final: 0.6159 (mmt) REVERT: C 452 TRP cc_start: 0.5628 (t60) cc_final: 0.5227 (t60) REVERT: C 514 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7445 (p) REVERT: C 692 ARG cc_start: 0.7029 (mtp180) cc_final: 0.5930 (mtt90) REVERT: C 699 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7233 (mt-10) REVERT: D 236 SER cc_start: 0.7928 (t) cc_final: 0.7424 (p) REVERT: D 452 TRP cc_start: 0.6424 (t60) cc_final: 0.5942 (t60) REVERT: D 514 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7591 (p) REVERT: D 526 MET cc_start: 0.6365 (mmm) cc_final: 0.5851 (mtt) REVERT: D 687 LEU cc_start: 0.5949 (OUTLIER) cc_final: 0.5451 (pp) REVERT: D 724 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6550 (mm-30) outliers start: 26 outliers final: 14 residues processed: 213 average time/residue: 0.2729 time to fit residues: 93.4844 Evaluate side-chains 215 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 644 SER Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 644 SER Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 644 SER Chi-restraints excluded: chain D residue 687 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.0010 chunk 231 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 193 optimal weight: 0.0060 chunk 20 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2970 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: