Starting phenix.real_space_refine on Wed Feb 14 06:53:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3a_35147/02_2024/8i3a_35147_updated.pdb" } resolution = 3.04 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= 0.001 sd= 0.140 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 5730 2.51 5 N 1476 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 401": "NH1" <-> "NH2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ASP 131": "OD1" <-> "OD2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 650": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8830 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4383 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 542} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.24, per 1000 atoms: 0.59 Number of scatterers: 8830 At special positions: 0 Unit cell: (75.53, 92.13, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 1562 8.00 N 1476 7.00 C 5730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 49.6% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.561A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.695A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 254 removed outlier: 3.791A pdb=" N LEU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 removed outlier: 3.674A pdb=" N GLN A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 269 through 274' Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.668A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.741A pdb=" N ALA A 384 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 424 removed outlier: 3.529A pdb=" N ALA A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 457 removed outlier: 3.600A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 439 " --> pdb=" O ASP A 435 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.504A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N PHE A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.668A pdb=" N ARG A 463 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A 464 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 469 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 472 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.677A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 removed outlier: 4.061A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 539 removed outlier: 3.539A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.909A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.656A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 657 removed outlier: 4.318A pdb=" N VAL A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.561A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.694A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.791A pdb=" N LEU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 removed outlier: 3.675A pdb=" N GLN B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 269 through 274' Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 358 removed outlier: 3.667A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 removed outlier: 3.741A pdb=" N ALA B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 424 removed outlier: 3.529A pdb=" N ALA B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.600A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 439 " --> pdb=" O ASP B 435 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.503A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.668A pdb=" N ARG B 463 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA B 464 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 469 " --> pdb=" O PHE B 466 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 472 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.678A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 506 removed outlier: 4.061A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 539 removed outlier: 3.539A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 removed outlier: 3.909A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 581 through 593 removed outlier: 3.656A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 657 removed outlier: 4.318A pdb=" N VAL B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 removed outlier: 5.350A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 285 through 291 removed outlier: 6.558A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 46 through 50 removed outlier: 7.086A pdb=" N VAL A 49 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR A 82 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 126 through 129 removed outlier: 5.350A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 285 through 291 removed outlier: 6.558A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 46 through 50 removed outlier: 7.086A pdb=" N VAL B 49 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR B 82 " --> pdb=" O VAL B 49 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1050 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: 2.51 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2366 1.33 - 1.45: 1730 1.45 - 1.57: 4826 1.57 - 1.70: 8 1.70 - 1.82: 88 Bond restraints: 9018 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.37e+01 bond pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 1.374 1.301 0.073 1.00e-02 1.00e+04 5.27e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.318 0.069 1.00e-02 1.00e+04 4.73e+01 bond pdb=" C5 ATP A 703 " pdb=" N7 ATP A 703 " ideal model delta sigma weight residual 1.387 1.319 0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C4' ATP A 701 " pdb=" O4' ATP A 701 " ideal model delta sigma weight residual 1.444 1.383 0.061 1.10e-02 8.26e+03 3.12e+01 ... (remaining 9013 not shown) Histogram of bond angle deviations from ideal: 90.38 - 99.47: 8 99.47 - 108.57: 512 108.57 - 117.66: 5993 117.66 - 126.76: 5598 126.76 - 135.85: 127 Bond angle restraints: 12238 Sorted by residual: angle pdb=" PB ATP A 703 " pdb=" O3B ATP A 703 " pdb=" PG ATP A 703 " ideal model delta sigma weight residual 139.87 129.18 10.69 1.00e+00 1.00e+00 1.14e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 129.21 10.66 1.00e+00 1.00e+00 1.14e+02 angle pdb=" N3 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N9 ATP A 701 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" N3 ATP A 703 " pdb=" C4 ATP A 703 " pdb=" N9 ATP A 703 " ideal model delta sigma weight residual 127.04 135.85 -8.81 1.15e+00 7.59e-01 5.89e+01 angle pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " ideal model delta sigma weight residual 101.57 113.31 -11.74 1.54e+00 4.24e-01 5.84e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4806 17.35 - 34.70: 443 34.70 - 52.05: 57 52.05 - 69.40: 24 69.40 - 86.75: 8 Dihedral angle restraints: 5338 sinusoidal: 2112 harmonic: 3226 Sorted by residual: dihedral pdb=" CA ALA B 297 " pdb=" C ALA B 297 " pdb=" N TYR B 298 " pdb=" CA TYR B 298 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ALA A 297 " pdb=" C ALA A 297 " pdb=" N TYR A 298 " pdb=" CA TYR A 298 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LEU B 169 " pdb=" C LEU B 169 " pdb=" N PRO B 170 " pdb=" CA PRO B 170 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1159 0.062 - 0.125: 240 0.125 - 0.187: 50 0.187 - 0.250: 2 0.250 - 0.312: 3 Chirality restraints: 1454 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASN B 567 " pdb=" N ASN B 567 " pdb=" C ASN B 567 " pdb=" CB ASN B 567 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1451 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 223 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE B 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 223 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 223 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C ILE A 223 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 223 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 224 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 101 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO B 102 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.030 5.00e-02 4.00e+02 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 33 2.60 - 3.17: 6713 3.17 - 3.75: 13047 3.75 - 4.32: 19641 4.32 - 4.90: 32453 Nonbonded interactions: 71887 Sorted by model distance: nonbonded pdb=" O2' ATP A 701 " pdb=" O3' ATP A 701 " model vdw 2.023 2.432 nonbonded pdb=" O2' ATP A 703 " pdb=" O3' ATP A 703 " model vdw 2.024 2.432 nonbonded pdb=" OH TYR B 152 " pdb=" OE1 GLU B 462 " model vdw 2.356 2.440 nonbonded pdb=" OH TYR A 152 " pdb=" OE1 GLU A 462 " model vdw 2.357 2.440 nonbonded pdb=" OG SER B 108 " pdb="MG MG B 701 " model vdw 2.377 2.170 ... (remaining 71882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 32 through 662) selection = (chain 'B' and resid 32 through 662) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.270 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.008 0.096 9018 Z= 0.490 Angle : 1.044 17.692 12238 Z= 0.608 Chirality : 0.056 0.312 1454 Planarity : 0.006 0.054 1488 Dihedral : 14.216 86.745 3262 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.61 % Favored : 92.21 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -4.99 (0.17), residues: 1104 helix: -3.22 (0.13), residues: 634 sheet: -1.97 (0.44), residues: 94 loop : -3.47 (0.24), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.006 0.001 HIS B 219 PHE 0.022 0.002 PHE B 499 TYR 0.018 0.002 TYR B 594 ARG 0.004 0.000 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.015 Fit side-chains REVERT: A 141 ARG cc_start: 0.7547 (mtm180) cc_final: 0.6813 (mmm160) REVERT: A 212 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7705 (ttp80) REVERT: A 285 LYS cc_start: 0.8043 (mttp) cc_final: 0.7724 (mtpt) REVERT: A 462 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 568 LYS cc_start: 0.7914 (tptp) cc_final: 0.7321 (mtpt) REVERT: B 141 ARG cc_start: 0.7573 (mtm180) cc_final: 0.6874 (mmm160) REVERT: B 212 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7720 (ttp80) REVERT: B 274 MET cc_start: 0.8779 (mtt) cc_final: 0.8527 (mtp) REVERT: B 285 LYS cc_start: 0.8018 (mttp) cc_final: 0.7706 (mtpt) REVERT: B 402 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7206 (ttm170) REVERT: B 462 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 568 LYS cc_start: 0.8535 (mttt) cc_final: 0.8283 (mtpt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3110 time to fit residues: 55.8855 Evaluate side-chains 116 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 254 HIS A 265 HIS A 352 GLN B 112 ASN B 147 GLN B 254 HIS B 265 HIS B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.185 Angle : 0.525 6.430 12238 Z= 0.271 Chirality : 0.040 0.143 1454 Planarity : 0.004 0.039 1488 Dihedral : 8.383 60.257 1282 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.98 % Favored : 93.84 % Rotamer: Outliers : 0.94 % Allowed : 6.56 % Favored : 92.50 % 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: -3.19 (0.22), residues: 1104 helix: -1.54 (0.18), residues: 632 sheet: -1.86 (0.48), residues: 82 loop : -2.96 (0.26), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.005 0.001 HIS B 434 PHE 0.013 0.001 PHE A 42 TYR 0.011 0.001 TYR B 594 ARG 0.002 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.958 Fit side-chains REVERT: A 133 LYS cc_start: 0.8393 (ptmm) cc_final: 0.8140 (ptmm) REVERT: A 141 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6783 (mmm160) REVERT: A 193 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8325 (mmmt) REVERT: A 429 ASP cc_start: 0.7814 (t70) cc_final: 0.7438 (t70) REVERT: A 568 LYS cc_start: 0.8028 (tptp) cc_final: 0.7392 (mtpt) REVERT: B 141 ARG cc_start: 0.7503 (mtm180) cc_final: 0.6750 (mmm160) REVERT: B 402 ARG cc_start: 0.7435 (ttm170) cc_final: 0.7108 (ttm170) REVERT: B 429 ASP cc_start: 0.7854 (t70) cc_final: 0.7522 (t70) REVERT: B 661 LYS cc_start: 0.7419 (mttt) cc_final: 0.7171 (mttm) outliers start: 9 outliers final: 8 residues processed: 131 average time/residue: 0.2874 time to fit residues: 48.4534 Evaluate side-chains 130 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 269 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 352 GLN A 434 HIS A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 9018 Z= 0.456 Angle : 0.661 6.593 12238 Z= 0.332 Chirality : 0.047 0.172 1454 Planarity : 0.004 0.039 1488 Dihedral : 8.586 61.139 1282 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.97 % Favored : 91.85 % Rotamer: Outliers : 1.77 % Allowed : 8.23 % Favored : 90.00 % 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: -2.92 (0.22), residues: 1104 helix: -1.38 (0.19), residues: 648 sheet: -1.58 (0.51), residues: 82 loop : -2.83 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 447 HIS 0.006 0.002 HIS A 434 PHE 0.018 0.002 PHE A 499 TYR 0.019 0.002 TYR B 594 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.055 Fit side-chains REVERT: A 141 ARG cc_start: 0.7550 (mtm180) cc_final: 0.6814 (mmm160) REVERT: A 285 LYS cc_start: 0.7897 (mttp) cc_final: 0.7595 (mmtt) REVERT: A 397 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8499 (tt) REVERT: A 568 LYS cc_start: 0.8125 (tptp) cc_final: 0.7518 (mttt) REVERT: B 141 ARG cc_start: 0.7539 (mtm180) cc_final: 0.6916 (mmm160) REVERT: B 285 LYS cc_start: 0.7909 (mttp) cc_final: 0.7600 (mmtt) REVERT: B 397 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8508 (tt) REVERT: B 568 LYS cc_start: 0.8372 (mttt) cc_final: 0.7939 (mtmt) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.2900 time to fit residues: 48.9840 Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 397 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9018 Z= 0.249 Angle : 0.542 6.804 12238 Z= 0.278 Chirality : 0.042 0.147 1454 Planarity : 0.004 0.037 1488 Dihedral : 8.258 64.870 1282 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 1.77 % Allowed : 10.21 % Favored : 88.02 % 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: -2.30 (0.24), residues: 1104 helix: -0.76 (0.20), residues: 630 sheet: -1.25 (0.56), residues: 76 loop : -2.76 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 447 HIS 0.005 0.001 HIS B 265 PHE 0.014 0.001 PHE A 499 TYR 0.013 0.001 TYR A 594 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 0.980 Fit side-chains REVERT: A 141 ARG cc_start: 0.7505 (mtm180) cc_final: 0.6874 (mmm160) REVERT: A 285 LYS cc_start: 0.7856 (mttp) cc_final: 0.7564 (mmtt) REVERT: A 568 LYS cc_start: 0.8141 (tptp) cc_final: 0.7519 (mttt) REVERT: B 141 ARG cc_start: 0.7498 (mtm180) cc_final: 0.6888 (mmm160) REVERT: B 285 LYS cc_start: 0.7868 (mttp) cc_final: 0.7553 (mmtt) REVERT: B 568 LYS cc_start: 0.8380 (mttt) cc_final: 0.7923 (mtpt) outliers start: 17 outliers final: 11 residues processed: 130 average time/residue: 0.2928 time to fit residues: 49.1803 Evaluate side-chains 127 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9018 Z= 0.177 Angle : 0.507 6.715 12238 Z= 0.259 Chirality : 0.040 0.137 1454 Planarity : 0.003 0.035 1488 Dihedral : 7.820 60.071 1282 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.70 % Favored : 93.12 % Rotamer: Outliers : 1.46 % Allowed : 11.77 % Favored : 86.77 % 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: -1.70 (0.24), residues: 1104 helix: -0.28 (0.21), residues: 626 sheet: -1.20 (0.57), residues: 76 loop : -2.41 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 447 HIS 0.006 0.001 HIS B 265 PHE 0.012 0.001 PHE A 499 TYR 0.010 0.001 TYR A 594 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.988 Fit side-chains REVERT: A 141 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6882 (mmm160) REVERT: A 193 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8423 (mmmt) REVERT: A 568 LYS cc_start: 0.8156 (tptp) cc_final: 0.7535 (mttt) REVERT: B 141 ARG cc_start: 0.7493 (mtm180) cc_final: 0.6886 (mmm160) REVERT: B 285 LYS cc_start: 0.7900 (mttp) cc_final: 0.7574 (mmtt) REVERT: B 568 LYS cc_start: 0.8394 (mttt) cc_final: 0.7948 (mtpt) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 0.2763 time to fit residues: 47.1839 Evaluate side-chains 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 130 ASN B 352 GLN B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 9018 Z= 0.392 Angle : 0.617 6.861 12238 Z= 0.309 Chirality : 0.045 0.169 1454 Planarity : 0.004 0.033 1488 Dihedral : 8.682 72.948 1282 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.34 % Favored : 92.48 % Rotamer: Outliers : 1.88 % Allowed : 12.08 % Favored : 86.04 % 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: -2.04 (0.24), residues: 1104 helix: -0.66 (0.20), residues: 644 sheet: -1.15 (0.56), residues: 80 loop : -2.48 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 447 HIS 0.008 0.001 HIS B 265 PHE 0.017 0.002 PHE B 499 TYR 0.017 0.002 TYR A 594 ARG 0.003 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.070 Fit side-chains REVERT: A 141 ARG cc_start: 0.7535 (mtm180) cc_final: 0.6969 (mmm160) REVERT: A 237 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8997 (mt) REVERT: A 285 LYS cc_start: 0.7925 (mttp) cc_final: 0.7689 (mttt) REVERT: B 141 ARG cc_start: 0.7534 (mtm180) cc_final: 0.6971 (mmm160) REVERT: B 237 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8984 (mt) REVERT: B 285 LYS cc_start: 0.7927 (mttp) cc_final: 0.7673 (mttt) REVERT: B 420 LEU cc_start: 0.8170 (tp) cc_final: 0.7936 (tp) REVERT: B 568 LYS cc_start: 0.8397 (mttt) cc_final: 0.7936 (mtmt) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.2955 time to fit residues: 50.2975 Evaluate side-chains 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN A 662 HIS B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.163 Angle : 0.500 6.717 12238 Z= 0.255 Chirality : 0.040 0.135 1454 Planarity : 0.003 0.034 1488 Dihedral : 7.887 64.011 1282 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.07 % Favored : 93.75 % Rotamer: Outliers : 1.56 % Allowed : 12.50 % Favored : 85.94 % 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: -1.43 (0.24), residues: 1104 helix: -0.05 (0.21), residues: 626 sheet: -1.08 (0.58), residues: 76 loop : -2.32 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 447 HIS 0.007 0.001 HIS B 265 PHE 0.012 0.001 PHE B 499 TYR 0.009 0.001 TYR A 594 ARG 0.002 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.987 Fit side-chains REVERT: A 141 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6912 (mmm160) REVERT: A 193 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8445 (mmmt) REVERT: A 285 LYS cc_start: 0.7869 (mttp) cc_final: 0.7596 (mmtt) REVERT: A 402 ARG cc_start: 0.7394 (ttm170) cc_final: 0.7117 (mtm-85) REVERT: A 420 LEU cc_start: 0.8032 (tp) cc_final: 0.7733 (mp) REVERT: A 568 LYS cc_start: 0.8147 (tptp) cc_final: 0.7531 (mttt) REVERT: B 141 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6908 (mmm160) REVERT: B 193 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8443 (mmmt) REVERT: B 285 LYS cc_start: 0.7860 (mttp) cc_final: 0.7583 (mmtt) REVERT: B 402 ARG cc_start: 0.7353 (ttm170) cc_final: 0.7066 (mtm-85) REVERT: B 568 LYS cc_start: 0.8380 (mttt) cc_final: 0.7928 (mtmt) outliers start: 15 outliers final: 13 residues processed: 133 average time/residue: 0.2880 time to fit residues: 49.1881 Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9018 Z= 0.196 Angle : 0.519 6.919 12238 Z= 0.263 Chirality : 0.041 0.140 1454 Planarity : 0.003 0.033 1488 Dihedral : 7.807 64.080 1282 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 1.46 % Allowed : 13.44 % Favored : 85.10 % 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 (0.25), residues: 1104 helix: 0.15 (0.21), residues: 614 sheet: -1.08 (0.57), residues: 76 loop : -2.16 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.008 0.001 HIS B 265 PHE 0.012 0.001 PHE B 499 TYR 0.011 0.001 TYR A 594 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 0.936 Fit side-chains REVERT: A 141 ARG cc_start: 0.7511 (mtm180) cc_final: 0.6927 (mmm160) REVERT: A 285 LYS cc_start: 0.7873 (mttp) cc_final: 0.7606 (mmtt) REVERT: A 402 ARG cc_start: 0.7426 (ttm170) cc_final: 0.7155 (mtm-85) REVERT: A 420 LEU cc_start: 0.8036 (tp) cc_final: 0.7736 (mp) REVERT: A 568 LYS cc_start: 0.8147 (tptp) cc_final: 0.7527 (mttt) REVERT: B 141 ARG cc_start: 0.7500 (mtm180) cc_final: 0.6923 (mmm160) REVERT: B 402 ARG cc_start: 0.7368 (ttm170) cc_final: 0.7095 (mtm-85) REVERT: B 568 LYS cc_start: 0.8357 (mttt) cc_final: 0.7918 (mtmt) outliers start: 14 outliers final: 13 residues processed: 130 average time/residue: 0.2750 time to fit residues: 46.6566 Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9018 Z= 0.219 Angle : 0.547 15.489 12238 Z= 0.271 Chirality : 0.041 0.143 1454 Planarity : 0.003 0.031 1488 Dihedral : 7.784 61.840 1282 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.34 % Favored : 93.48 % Rotamer: Outliers : 1.46 % Allowed : 14.06 % Favored : 84.48 % 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: -1.26 (0.25), residues: 1104 helix: 0.13 (0.21), residues: 616 sheet: -1.05 (0.57), residues: 76 loop : -2.26 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.009 0.001 HIS B 265 PHE 0.013 0.001 PHE A 499 TYR 0.011 0.001 TYR A 594 ARG 0.006 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 0.991 Fit side-chains REVERT: A 141 ARG cc_start: 0.7490 (mtm180) cc_final: 0.6922 (mmm160) REVERT: A 285 LYS cc_start: 0.7875 (mttp) cc_final: 0.7627 (mmtt) REVERT: A 401 ARG cc_start: 0.7878 (mtm-85) cc_final: 0.7513 (ptp-170) REVERT: A 402 ARG cc_start: 0.7422 (ttm170) cc_final: 0.7168 (mtm-85) REVERT: A 420 LEU cc_start: 0.8028 (tp) cc_final: 0.7718 (mp) REVERT: A 568 LYS cc_start: 0.8138 (tptp) cc_final: 0.7524 (mttt) REVERT: B 141 ARG cc_start: 0.7489 (mtm180) cc_final: 0.6941 (mmm160) REVERT: B 285 LYS cc_start: 0.7893 (mttp) cc_final: 0.7628 (mmtt) REVERT: B 401 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7520 (ptp-170) REVERT: B 420 LEU cc_start: 0.8026 (tp) cc_final: 0.7698 (mp) REVERT: B 568 LYS cc_start: 0.8383 (mttt) cc_final: 0.7924 (mtmt) outliers start: 14 outliers final: 14 residues processed: 132 average time/residue: 0.2883 time to fit residues: 49.2311 Evaluate side-chains 133 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9018 Z= 0.178 Angle : 0.527 16.260 12238 Z= 0.261 Chirality : 0.040 0.139 1454 Planarity : 0.003 0.032 1488 Dihedral : 7.448 55.701 1282 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.98 % Favored : 93.84 % Rotamer: Outliers : 1.25 % Allowed : 14.17 % Favored : 84.58 % 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: -1.09 (0.25), residues: 1104 helix: 0.22 (0.21), residues: 626 sheet: -1.02 (0.57), residues: 76 loop : -2.15 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.008 0.001 HIS B 265 PHE 0.012 0.001 PHE A 499 TYR 0.010 0.001 TYR A 594 ARG 0.005 0.000 ARG B 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.990 Fit side-chains REVERT: A 141 ARG cc_start: 0.7498 (mtm180) cc_final: 0.6931 (mmm160) REVERT: A 285 LYS cc_start: 0.7883 (mttp) cc_final: 0.7625 (mmtt) REVERT: A 568 LYS cc_start: 0.8136 (tptp) cc_final: 0.7526 (mttt) REVERT: B 141 ARG cc_start: 0.7472 (mtm180) cc_final: 0.6931 (mmm160) REVERT: B 402 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7186 (mtm-85) REVERT: B 568 LYS cc_start: 0.8379 (mttt) cc_final: 0.7929 (mtmt) outliers start: 12 outliers final: 11 residues processed: 125 average time/residue: 0.2724 time to fit residues: 44.6551 Evaluate side-chains 127 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 GLN A 454 ASN B 352 GLN B 434 HIS B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102957 restraints weight = 9035.322| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.96 r_work: 0.3027 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9018 Z= 0.163 Angle : 0.516 15.095 12238 Z= 0.256 Chirality : 0.040 0.136 1454 Planarity : 0.003 0.032 1488 Dihedral : 7.201 50.927 1282 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.53 % Favored : 94.29 % Rotamer: Outliers : 1.35 % Allowed : 13.96 % Favored : 84.69 % 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: -0.86 (0.25), residues: 1104 helix: 0.43 (0.21), residues: 614 sheet: -0.93 (0.57), residues: 76 loop : -2.02 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 447 HIS 0.008 0.001 HIS B 265 PHE 0.011 0.001 PHE A 499 TYR 0.009 0.001 TYR B 594 ARG 0.003 0.000 ARG B 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2098.85 seconds wall clock time: 38 minutes 41.21 seconds (2321.21 seconds total)