Starting phenix.real_space_refine on Thu Sep 26 10:03:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dd6_30645/09_2024/7dd6_30645.cif" } resolution = 3.2 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= 0.091 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 Ca 6 9.91 5 S 70 5.16 5 Cl 2 4.86 5 C 8213 2.51 5 N 2028 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12678 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6209 Classifications: {'peptide': 791} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PTRANS': 34, 'TRANS': 756} Chain breaks: 3 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 6235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6235 Classifications: {'peptide': 792} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 33, 'TRANS': 758} Chain breaks: 3 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 61 Unusual residues: {' CA': 3, ' CL': 1, 'NAG': 3} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.19, per 1000 atoms: 0.65 Number of scatterers: 12678 At special positions: 0 Unit cell: (100.386, 93.288, 182.52, 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) Ca 6 19.99 Cl 2 17.00 S 70 16.00 O 2359 8.00 N 2028 7.00 C 8213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.73 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 448 " distance=2.24 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 561 " distance=2.02 Simple disulfide: pdb=" SG CYS A 545 " - pdb=" SG CYS A 564 " distance=2.04 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 584 " - pdb=" SG CYS A 597 " distance=2.49 Simple disulfide: pdb=" SG CYS A 676 " - pdb=" SG CYS A 764 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 448 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 561 " distance=2.66 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 584 " - pdb=" SG CYS B 597 " distance=1.82 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 764 " distance=2.39 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1105 " - " ASN A 287 " " NAG A1106 " - " ASN A 399 " " NAG A1107 " - " ASN A 467 " " NAG B1105 " - " ASN B 287 " " NAG B1106 " - " ASN B 399 " " NAG B1107 " - " ASN B 467 " " NAG C 1 " - " ASN A 487 " " NAG D 1 " - " ASN A 540 " " NAG E 1 " - " ASN B 487 " " NAG F 1 " - " ASN B 540 " Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 16 sheets defined 49.5% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.641A pdb=" N ALA A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.712A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.707A pdb=" N LEU A 174 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.561A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 307 through 315 removed outlier: 4.387A pdb=" N VAL A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 399 through 403 removed outlier: 3.780A pdb=" N VAL A 403 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 435 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.594A pdb=" N LYS A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 454 " --> pdb=" O ILE A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 454' Processing helix chain 'A' and resid 455 through 465 removed outlier: 3.526A pdb=" N HIS A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 609 through 636 Processing helix chain 'A' and resid 639 through 644 removed outlier: 4.209A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.557A pdb=" N ILE A 668 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 697 removed outlier: 3.577A pdb=" N CYS A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Proline residue: A 681 - end of helix Processing helix chain 'A' and resid 700 through 706 Processing helix chain 'A' and resid 720 through 745 removed outlier: 3.605A pdb=" N LEU A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE A 732 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 792 Processing helix chain 'A' and resid 801 through 826 removed outlier: 4.163A pdb=" N PHE A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Proline residue: A 822 - end of helix removed outlier: 3.552A pdb=" N SER A 826 " --> pdb=" O PRO A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 862 removed outlier: 3.798A pdb=" N SER A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN A 854 " --> pdb=" O CYS A 850 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS A 855 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.728A pdb=" N ALA B 107 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 146 through 158 removed outlier: 4.027A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.643A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.530A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.913A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 296 through 301 removed outlier: 4.501A pdb=" N SER B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.703A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.733A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 450 through 454 removed outlier: 3.621A pdb=" N LYS B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 450 through 454' Processing helix chain 'B' and resid 455 through 465 removed outlier: 3.617A pdb=" N HIS B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 636 Processing helix chain 'B' and resid 639 through 644 removed outlier: 4.097A pdb=" N LYS B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 664 through 668 removed outlier: 3.626A pdb=" N ILE B 668 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 697 Proline residue: B 681 - end of helix Processing helix chain 'B' and resid 700 through 706 Processing helix chain 'B' and resid 720 through 743 removed outlier: 4.080A pdb=" N PHE B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 726 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 727 " --> pdb=" O GLN B 723 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE B 732 " --> pdb=" O PHE B 728 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 737 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 793 removed outlier: 3.603A pdb=" N SER B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.978A pdb=" N PHE B 805 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Proline residue: B 822 - end of helix Processing helix chain 'B' and resid 828 through 862 removed outlier: 3.615A pdb=" N SER B 833 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN B 854 " --> pdb=" O CYS B 850 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.103A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.819A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.983A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 320 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N THR A 317 " --> pdb=" O TRP A 493 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 488 " --> pdb=" O HIS A 509 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS A 509 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 490 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'A' and resid 549 through 553 Processing sheet with id=AA6, first strand: chain 'A' and resid 571 through 572 Processing sheet with id=AA7, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA8, first strand: chain 'A' and resid 601 through 603 removed outlier: 6.751A pdb=" N GLN A 601 " --> pdb=" O ILE A 760 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ILE A 762 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N GLU A 603 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N CYS A 764 " --> pdb=" O GLU A 603 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.971A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 33 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL B 142 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 35 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.849A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.919A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TRP B 208 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL B 268 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY B 210 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE B 270 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 212 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP B 293 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE B 320 " --> pdb=" O TRP B 293 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA B 295 " --> pdb=" O PHE B 320 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR B 317 " --> pdb=" O TRP B 493 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 488 " --> pdb=" O HIS B 509 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS B 509 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 490 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 469 Processing sheet with id=AB4, first strand: chain 'B' and resid 549 through 552 Processing sheet with id=AB5, first strand: chain 'B' and resid 571 through 572 Processing sheet with id=AB6, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 603 removed outlier: 4.117A pdb=" N ILE B 762 " --> pdb=" O GLU B 603 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1722 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: 4.54 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2054 1.31 - 1.44: 3635 1.44 - 1.57: 7216 1.57 - 1.70: 0 1.70 - 1.83: 86 Bond restraints: 12991 Sorted by residual: bond pdb=" C7 NAG A1107 " pdb=" N2 NAG A1107 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C7 NAG B1105 " pdb=" N2 NAG B1105 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C7 NAG B1106 " pdb=" N2 NAG B1106 " ideal model delta sigma weight residual 1.346 1.453 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C7 NAG B1107 " pdb=" N2 NAG B1107 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 17096 2.03 - 4.07: 443 4.07 - 6.10: 81 6.10 - 8.14: 17 8.14 - 10.17: 4 Bond angle restraints: 17641 Sorted by residual: angle pdb=" C THR B 698 " pdb=" N ASN B 699 " pdb=" CA ASN B 699 " ideal model delta sigma weight residual 120.71 127.74 -7.03 1.42e+00 4.96e-01 2.45e+01 angle pdb=" C ILE B 740 " pdb=" N TRP B 741 " pdb=" CA TRP B 741 " ideal model delta sigma weight residual 120.28 114.96 5.32 1.34e+00 5.57e-01 1.58e+01 angle pdb=" CA ARG B 700 " pdb=" C ARG B 700 " pdb=" O ARG B 700 " ideal model delta sigma weight residual 122.44 117.38 5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" CA ARG A 700 " pdb=" C ARG A 700 " pdb=" O ARG A 700 " ideal model delta sigma weight residual 122.44 117.39 5.05 1.34e+00 5.57e-01 1.42e+01 angle pdb=" N LYS A 697 " pdb=" CA LYS A 697 " pdb=" C LYS A 697 " ideal model delta sigma weight residual 113.21 109.06 4.15 1.15e+00 7.56e-01 1.30e+01 ... (remaining 17636 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.36: 7193 23.36 - 46.72: 510 46.72 - 70.08: 89 70.08 - 93.44: 30 93.44 - 116.80: 7 Dihedral angle restraints: 7829 sinusoidal: 3225 harmonic: 4604 Sorted by residual: dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual 93.00 -178.39 -88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 676 " pdb=" SG CYS B 676 " pdb=" SG CYS B 764 " pdb=" CB CYS B 764 " ideal model delta sinusoidal sigma weight residual 93.00 7.40 85.60 1 1.00e+01 1.00e-02 8.86e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual 93.00 16.54 76.46 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 7826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1921 0.105 - 0.210: 80 0.210 - 0.315: 3 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 2005 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.78e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 487 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA VAL A 704 " pdb=" N VAL A 704 " pdb=" C VAL A 704 " pdb=" CB VAL A 704 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2002 not shown) Planarity restraints: 2239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 697 " 0.024 2.00e-02 2.50e+03 4.74e-02 2.24e+01 pdb=" C LYS B 697 " -0.082 2.00e-02 2.50e+03 pdb=" O LYS B 697 " 0.031 2.00e-02 2.50e+03 pdb=" N THR B 698 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 670 " -0.034 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO B 671 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 671 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 671 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO A 188 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " 0.024 5.00e-02 4.00e+02 ... (remaining 2236 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 374 2.68 - 3.24: 13018 3.24 - 3.79: 19599 3.79 - 4.35: 25818 4.35 - 4.90: 42025 Nonbonded interactions: 100834 Sorted by model distance: nonbonded pdb=" O LEU B 430 " pdb=" CG2 ILE B 433 " model vdw 2.126 3.460 nonbonded pdb=" O ILE B 623 " pdb=" OG1 THR B 626 " model vdw 2.147 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O TRP B1108 " model vdw 2.153 3.040 nonbonded pdb=" O ALA A 110 " pdb=" OG SER A 113 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 150 " pdb=" OG SER B 169 " model vdw 2.192 3.040 ... (remaining 100829 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 22 through 119 or resid 136 through 867 or resid 1101 thro \ ugh 1108)) selection = (chain 'B' and (resid 22 through 119 or resid 136 through 358 or (resid 359 and \ (name N or name CA or name C or name O or name CB )) or resid 392 through 867 or \ resid 1101 through 1108)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.110 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.490 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 0.107 12991 Z= 0.526 Angle : 0.809 10.169 17641 Z= 0.451 Chirality : 0.050 0.525 2005 Planarity : 0.004 0.051 2229 Dihedral : 16.894 116.801 4798 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.07 % Allowed : 20.34 % Favored : 79.58 % 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: -3.07 (0.18), residues: 1567 helix: -1.20 (0.17), residues: 685 sheet: -2.17 (0.37), residues: 153 loop : -2.84 (0.18), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 765 PHE 0.015 0.001 PHE B 562 TYR 0.014 0.001 TYR A 750 ARG 0.004 0.000 ARG B 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9125 (tp) cc_final: 0.8882 (tt) REVERT: A 571 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 587 ASP cc_start: 0.8364 (p0) cc_final: 0.7842 (t0) REVERT: A 756 GLU cc_start: 0.7753 (tp30) cc_final: 0.7148 (tp30) REVERT: A 810 MET cc_start: 0.6302 (mtm) cc_final: 0.5673 (mtm) REVERT: A 813 PHE cc_start: 0.6804 (t80) cc_final: 0.6536 (t80) REVERT: B 472 MET cc_start: 0.8335 (mtm) cc_final: 0.8129 (mtm) REVERT: B 752 ASN cc_start: 0.8592 (t0) cc_final: 0.8192 (m110) REVERT: B 787 PHE cc_start: 0.7982 (t80) cc_final: 0.7728 (t80) REVERT: B 800 PHE cc_start: 0.8809 (m-10) cc_final: 0.8290 (m-80) REVERT: B 805 PHE cc_start: 0.8393 (m-80) cc_final: 0.7817 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2533 time to fit residues: 71.1353 Evaluate side-chains 105 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 741 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 335 GLN A 465 HIS ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 HIS A 672 GLN A 734 GLN A 752 ASN A 799 ASN B 23 ASN B 118 ASN B 193 GLN B 245 GLN B 260 GLN B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS B 494 HIS B 509 HIS B 734 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12991 Z= 0.238 Angle : 0.673 11.623 17641 Z= 0.338 Chirality : 0.049 0.703 2005 Planarity : 0.005 0.063 2229 Dihedral : 9.596 109.832 1975 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.19 % Allowed : 20.64 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.20), residues: 1567 helix: 0.05 (0.19), residues: 708 sheet: -1.64 (0.37), residues: 177 loop : -2.29 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 674 HIS 0.003 0.001 HIS A 594 PHE 0.039 0.002 PHE A 814 TYR 0.012 0.001 TYR B 651 ARG 0.006 0.001 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 117 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9073 (tp) cc_final: 0.8800 (tt) REVERT: A 587 ASP cc_start: 0.8189 (p0) cc_final: 0.7763 (t0) REVERT: A 641 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6088 (mt) REVERT: A 751 ARG cc_start: 0.7440 (ptm160) cc_final: 0.6461 (ptm160) REVERT: A 752 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8165 (t0) REVERT: A 756 GLU cc_start: 0.7717 (tp30) cc_final: 0.7154 (tp30) REVERT: A 810 MET cc_start: 0.6023 (mtm) cc_final: 0.5722 (mtm) REVERT: A 845 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: B 462 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7945 (m170) REVERT: B 586 GLU cc_start: 0.8761 (mp0) cc_final: 0.8540 (mp0) REVERT: B 741 TRP cc_start: 0.5613 (t60) cc_final: 0.5279 (t60) REVERT: B 787 PHE cc_start: 0.8086 (t80) cc_final: 0.7811 (t80) outliers start: 43 outliers final: 20 residues processed: 149 average time/residue: 0.1953 time to fit residues: 46.0309 Evaluate side-chains 121 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 792 LYS Chi-restraints excluded: chain A residue 828 TYR Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 674 TRP Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 837 VAL Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 143 optimal weight: 0.0980 chunk 155 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12991 Z= 0.169 Angle : 0.603 9.482 17641 Z= 0.300 Chirality : 0.047 0.678 2005 Planarity : 0.004 0.065 2229 Dihedral : 7.874 107.636 1973 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.52 % Allowed : 20.79 % Favored : 76.69 % 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: -1.06 (0.20), residues: 1567 helix: 0.59 (0.19), residues: 710 sheet: -1.25 (0.39), residues: 178 loop : -1.97 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.002 0.000 HIS B 753 PHE 0.020 0.001 PHE B 633 TYR 0.009 0.001 TYR B 651 ARG 0.007 0.000 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 587 ASP cc_start: 0.8126 (p0) cc_final: 0.7657 (t0) REVERT: A 641 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6355 (mt) REVERT: A 756 GLU cc_start: 0.7743 (tp30) cc_final: 0.7222 (tp30) REVERT: A 845 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: B 462 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (m170) outliers start: 34 outliers final: 15 residues processed: 127 average time/residue: 0.2011 time to fit residues: 40.6361 Evaluate side-chains 112 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 752 ASN B 335 GLN ** B 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12991 Z= 0.314 Angle : 0.637 10.711 17641 Z= 0.319 Chirality : 0.049 0.707 2005 Planarity : 0.004 0.067 2229 Dihedral : 7.562 106.815 1973 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.16 % Allowed : 20.64 % Favored : 75.20 % 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: -0.76 (0.21), residues: 1567 helix: 0.82 (0.19), residues: 709 sheet: -0.98 (0.41), residues: 174 loop : -1.82 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 299 HIS 0.004 0.001 HIS A 192 PHE 0.025 0.002 PHE A 774 TYR 0.012 0.001 TYR B 417 ARG 0.003 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 102 time to evaluate : 1.688 Fit side-chains REVERT: A 587 ASP cc_start: 0.8204 (p0) cc_final: 0.7752 (t0) REVERT: A 641 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6739 (mt) REVERT: A 751 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8119 (mmm-85) REVERT: A 752 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7903 (t0) REVERT: A 756 GLU cc_start: 0.7707 (tp30) cc_final: 0.7178 (tp30) REVERT: A 810 MET cc_start: 0.6643 (mtm) cc_final: 0.6307 (mtt) REVERT: A 814 PHE cc_start: 0.8054 (m-80) cc_final: 0.7788 (m-80) REVERT: A 845 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: B 307 MET cc_start: 0.7676 (mtp) cc_final: 0.7105 (mtt) REVERT: B 725 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7977 (mt) outliers start: 56 outliers final: 27 residues processed: 149 average time/residue: 0.2087 time to fit residues: 48.9394 Evaluate side-chains 122 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 105 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 ASN B 335 GLN B 338 HIS ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 12991 Z= 0.191 Angle : 0.592 14.067 17641 Z= 0.291 Chirality : 0.047 0.706 2005 Planarity : 0.004 0.068 2229 Dihedral : 7.327 106.190 1973 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.04 % Allowed : 22.05 % Favored : 74.91 % 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: -0.52 (0.21), residues: 1567 helix: 1.00 (0.19), residues: 708 sheet: -0.90 (0.41), residues: 178 loop : -1.66 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 299 HIS 0.002 0.001 HIS B 494 PHE 0.025 0.001 PHE B 683 TYR 0.011 0.001 TYR B 417 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 98 time to evaluate : 1.510 Fit side-chains REVERT: A 587 ASP cc_start: 0.8217 (p0) cc_final: 0.7735 (t0) REVERT: A 751 ARG cc_start: 0.8497 (mtp180) cc_final: 0.8163 (mmm-85) REVERT: A 752 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7823 (t0) REVERT: A 756 GLU cc_start: 0.7773 (tp30) cc_final: 0.7236 (tp30) REVERT: A 808 PHE cc_start: 0.8222 (m-80) cc_final: 0.8015 (m-80) REVERT: A 845 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: B 307 MET cc_start: 0.7670 (mtp) cc_final: 0.7116 (mtt) outliers start: 41 outliers final: 29 residues processed: 129 average time/residue: 0.2099 time to fit residues: 43.5183 Evaluate side-chains 122 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 471 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 12991 Z= 0.430 Angle : 0.689 18.022 17641 Z= 0.344 Chirality : 0.051 0.736 2005 Planarity : 0.005 0.069 2229 Dihedral : 7.578 107.545 1973 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.53 % Allowed : 21.46 % Favored : 74.02 % 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: -0.64 (0.21), residues: 1567 helix: 0.98 (0.19), residues: 704 sheet: -1.36 (0.37), residues: 200 loop : -1.66 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 299 HIS 0.005 0.001 HIS B 753 PHE 0.027 0.002 PHE A 774 TYR 0.013 0.002 TYR B 417 ARG 0.004 0.001 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 91 time to evaluate : 1.403 Fit side-chains REVERT: A 587 ASP cc_start: 0.8403 (p0) cc_final: 0.7906 (t0) REVERT: A 751 ARG cc_start: 0.8476 (mtp180) cc_final: 0.8182 (mmm-85) REVERT: A 752 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8345 (t0) REVERT: A 756 GLU cc_start: 0.7921 (tp30) cc_final: 0.7333 (tp30) REVERT: A 810 MET cc_start: 0.6703 (mtt) cc_final: 0.6307 (mtm) REVERT: A 814 PHE cc_start: 0.7994 (m-80) cc_final: 0.7678 (m-80) REVERT: A 845 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: B 307 MET cc_start: 0.7827 (mtp) cc_final: 0.7306 (mtt) REVERT: B 698 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 725 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7973 (mt) outliers start: 61 outliers final: 44 residues processed: 139 average time/residue: 0.1918 time to fit residues: 42.8555 Evaluate side-chains 136 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 840 ILE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 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 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12991 Z= 0.186 Angle : 0.611 16.047 17641 Z= 0.298 Chirality : 0.048 0.713 2005 Planarity : 0.004 0.063 2229 Dihedral : 7.338 106.389 1973 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.27 % Allowed : 22.87 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1567 helix: 1.14 (0.19), residues: 707 sheet: -1.07 (0.38), residues: 184 loop : -1.55 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 299 HIS 0.002 0.001 HIS B 494 PHE 0.019 0.001 PHE B 788 TYR 0.010 0.001 TYR B 417 ARG 0.003 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 92 time to evaluate : 1.497 Fit side-chains REVERT: A 587 ASP cc_start: 0.8354 (p0) cc_final: 0.7843 (t0) REVERT: A 751 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8106 (mmm-85) REVERT: A 756 GLU cc_start: 0.7870 (tp30) cc_final: 0.7325 (tp30) REVERT: A 810 MET cc_start: 0.6662 (mtt) cc_final: 0.6281 (mtm) REVERT: A 814 PHE cc_start: 0.8084 (m-80) cc_final: 0.7759 (m-80) REVERT: A 845 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: B 307 MET cc_start: 0.7771 (mtp) cc_final: 0.7256 (mtt) REVERT: B 698 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 725 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7958 (mt) outliers start: 44 outliers final: 34 residues processed: 124 average time/residue: 0.1960 time to fit residues: 39.5880 Evaluate side-chains 124 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 87 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 424 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0970 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 0.0000 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 335 GLN ** A 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12991 Z= 0.177 Angle : 0.595 16.876 17641 Z= 0.287 Chirality : 0.047 0.676 2005 Planarity : 0.004 0.073 2229 Dihedral : 7.118 103.992 1973 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 23.24 % Favored : 73.42 % 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 (0.21), residues: 1567 helix: 1.22 (0.20), residues: 708 sheet: -0.86 (0.41), residues: 162 loop : -1.37 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 299 HIS 0.002 0.000 HIS B 494 PHE 0.036 0.001 PHE A 774 TYR 0.012 0.001 TYR A 824 ARG 0.002 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 93 time to evaluate : 1.479 Fit side-chains REVERT: A 307 MET cc_start: 0.8106 (mtp) cc_final: 0.7890 (mtt) REVERT: A 587 ASP cc_start: 0.8288 (p0) cc_final: 0.7718 (t0) REVERT: A 751 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8106 (mmm-85) REVERT: A 752 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8496 (t0) REVERT: A 756 GLU cc_start: 0.7904 (tp30) cc_final: 0.7338 (tp30) REVERT: A 810 MET cc_start: 0.6883 (mtt) cc_final: 0.6666 (mtm) REVERT: A 814 PHE cc_start: 0.8142 (m-80) cc_final: 0.7810 (m-80) REVERT: A 845 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: B 145 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 307 MET cc_start: 0.7734 (mtp) cc_final: 0.7199 (mtt) REVERT: B 571 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: B 605 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6586 (tp) REVERT: B 698 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 725 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8005 (mt) outliers start: 45 outliers final: 32 residues processed: 128 average time/residue: 0.2007 time to fit residues: 41.2590 Evaluate side-chains 126 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 87 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 504 PHE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12991 Z= 0.362 Angle : 0.656 17.468 17641 Z= 0.325 Chirality : 0.050 0.718 2005 Planarity : 0.004 0.074 2229 Dihedral : 7.313 105.160 1973 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.19 % Allowed : 23.31 % Favored : 73.50 % 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: -0.32 (0.21), residues: 1567 helix: 1.15 (0.19), residues: 702 sheet: -1.04 (0.37), residues: 195 loop : -1.43 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 753 PHE 0.025 0.001 PHE A 774 TYR 0.012 0.001 TYR B 203 ARG 0.011 0.001 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 86 time to evaluate : 1.462 Fit side-chains REVERT: A 587 ASP cc_start: 0.8325 (p0) cc_final: 0.7734 (t0) REVERT: A 751 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8113 (mmm-85) REVERT: A 756 GLU cc_start: 0.7913 (tp30) cc_final: 0.7229 (tp30) REVERT: A 810 MET cc_start: 0.6889 (mtt) cc_final: 0.6636 (mtm) REVERT: A 814 PHE cc_start: 0.8040 (m-80) cc_final: 0.7757 (m-80) REVERT: B 307 MET cc_start: 0.7803 (mtp) cc_final: 0.7293 (mtt) REVERT: B 571 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: B 605 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6604 (tp) REVERT: B 698 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 725 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8037 (mt) outliers start: 43 outliers final: 32 residues processed: 121 average time/residue: 0.1890 time to fit residues: 37.2542 Evaluate side-chains 122 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12991 Z= 0.344 Angle : 0.654 17.690 17641 Z= 0.323 Chirality : 0.050 0.725 2005 Planarity : 0.004 0.073 2229 Dihedral : 7.456 106.204 1973 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.90 % Allowed : 23.61 % Favored : 73.50 % 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: -0.39 (0.21), residues: 1567 helix: 1.11 (0.19), residues: 700 sheet: -1.12 (0.37), residues: 194 loop : -1.45 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 674 HIS 0.004 0.001 HIS B 753 PHE 0.027 0.001 PHE A 774 TYR 0.012 0.001 TYR B 203 ARG 0.006 0.000 ARG B 751 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3134 Ramachandran restraints generated. 1567 Oldfield, 0 Emsley, 1567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 1.452 Fit side-chains REVERT: A 756 GLU cc_start: 0.7878 (tp30) cc_final: 0.7077 (tp30) REVERT: A 810 MET cc_start: 0.7102 (mtt) cc_final: 0.6840 (mtm) REVERT: A 814 PHE cc_start: 0.7998 (m-80) cc_final: 0.7719 (m-80) REVERT: B 307 MET cc_start: 0.7799 (mtp) cc_final: 0.7284 (mtt) REVERT: B 571 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: B 605 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6653 (tp) REVERT: B 698 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (p) REVERT: B 725 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (mt) outliers start: 39 outliers final: 32 residues processed: 120 average time/residue: 0.1872 time to fit residues: 36.6053 Evaluate side-chains 123 residues out of total 1386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 87 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 571 GLU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 698 THR Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.124438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.082463 restraints weight = 26610.508| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.03 r_work: 0.3212 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12991 Z= 0.168 Angle : 0.604 17.922 17641 Z= 0.291 Chirality : 0.047 0.692 2005 Planarity : 0.004 0.072 2229 Dihedral : 7.187 104.337 1973 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.67 % Allowed : 23.98 % Favored : 73.35 % 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: -0.18 (0.21), residues: 1567 helix: 1.20 (0.19), residues: 703 sheet: -1.04 (0.38), residues: 184 loop : -1.26 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 299 HIS 0.002 0.000 HIS A 462 PHE 0.026 0.001 PHE A 774 TYR 0.011 0.001 TYR A 824 ARG 0.006 0.000 ARG B 751 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2527.57 seconds wall clock time: 46 minutes 6.24 seconds (2766.24 seconds total)