Starting phenix.real_space_refine on Wed Jul 30 22:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_30645.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_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/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_30645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_30645.map" model { file = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_30645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2025/7dd6_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-5711/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: 8.29, 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: 3.64 Conformation dependent library (CDL) restraints added in 1.7 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: 1.47 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: 4.30 Time building geometry restraints manager: 4.25 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.120 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- 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 : 0.013 0.701 13022 Z= 0.664 Angle : 1.056 49.632 17717 Z= 0.552 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 10) link_NAG-ASN : angle 3.51666 ( 30) link_BETA1-4 : bond 0.00479 ( 4) link_BETA1-4 : angle 1.05161 ( 12) hydrogen bonds : bond 0.13911 ( 594) hydrogen bonds : angle 6.70983 ( 1722) SS BOND : bond 0.27788 ( 17) SS BOND : angle 15.19897 ( 34) covalent geometry : bond 0.00829 (12991) covalent geometry : angle 0.80855 (17641) *********************** 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 to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.473 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: 0.2622 time to fit residues: 73.6174 Evaluate side-chains 105 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084159 restraints weight = 26858.605| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.24 r_work: 0.3177 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 13022 Z= 0.164 Angle : 0.696 15.381 17717 Z= 0.344 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00416 ( 10) link_NAG-ASN : angle 3.97649 ( 30) link_BETA1-4 : bond 0.00562 ( 4) link_BETA1-4 : angle 1.62895 ( 12) hydrogen bonds : bond 0.05600 ( 594) hydrogen bonds : angle 5.17616 ( 1722) SS BOND : bond 0.00521 ( 17) SS BOND : angle 1.54622 ( 34) covalent geometry : bond 0.00366 (12991) covalent geometry : angle 0.67282 (17641) *********************** 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 to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9093 (tp) cc_final: 0.8713 (tt) REVERT: A 587 ASP cc_start: 0.8838 (p0) cc_final: 0.8211 (t0) REVERT: A 641 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6154 (mt) REVERT: A 751 ARG cc_start: 0.7435 (ptm160) cc_final: 0.6444 (ptm160) REVERT: A 752 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8164 (t0) REVERT: A 756 GLU cc_start: 0.7954 (tp30) cc_final: 0.7255 (tp30) REVERT: A 810 MET cc_start: 0.5881 (mtm) cc_final: 0.5574 (mtm) REVERT: A 845 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: B 462 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7878 (m170) REVERT: B 472 MET cc_start: 0.8247 (mtm) cc_final: 0.8014 (mtm) REVERT: B 586 GLU cc_start: 0.9077 (mp0) cc_final: 0.8841 (mp0) REVERT: B 741 TRP cc_start: 0.5415 (t60) cc_final: 0.5162 (t60) REVERT: B 787 PHE cc_start: 0.8095 (t80) cc_final: 0.7799 (t80) outliers start: 43 outliers final: 20 residues processed: 149 average time/residue: 0.1971 time to fit residues: 46.6124 Evaluate side-chains 121 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.126390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084286 restraints weight = 27058.197| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.28 r_work: 0.3177 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13022 Z= 0.132 Angle : 0.631 15.544 17717 Z= 0.307 Chirality : 0.047 0.679 2005 Planarity : 0.004 0.064 2229 Dihedral : 7.868 107.781 1973 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.97 % Allowed : 20.64 % Favored : 76.39 % 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: -1.07 (0.20), residues: 1567 helix: 0.59 (0.19), residues: 708 sheet: -1.25 (0.39), residues: 179 loop : -1.99 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 299 HIS 0.003 0.001 HIS A 753 PHE 0.021 0.001 PHE B 633 TYR 0.009 0.001 TYR A 417 ARG 0.007 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 10) link_NAG-ASN : angle 4.13144 ( 30) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 1.61523 ( 12) hydrogen bonds : bond 0.04900 ( 594) hydrogen bonds : angle 4.85270 ( 1722) SS BOND : bond 0.00354 ( 17) SS BOND : angle 1.05214 ( 34) covalent geometry : bond 0.00282 (12991) covalent geometry : angle 0.60560 (17641) *********************** 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 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 103 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 257 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 504 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: A 587 ASP cc_start: 0.8828 (p0) cc_final: 0.8161 (t0) REVERT: A 641 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6471 (mt) REVERT: A 756 GLU cc_start: 0.8004 (tp30) cc_final: 0.7325 (tp30) REVERT: A 845 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: B 462 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7884 (m170) outliers start: 40 outliers final: 18 residues processed: 131 average time/residue: 0.1923 time to fit residues: 40.5133 Evaluate side-chains 118 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 150 SER 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 425 SER Chi-restraints excluded: chain A residue 504 PHE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 30 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 112 optimal weight: 0.0470 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- 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 ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.127548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.086291 restraints weight = 26798.925| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.06 r_work: 0.3280 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13022 Z= 0.108 Angle : 0.595 14.919 17717 Z= 0.285 Chirality : 0.046 0.670 2005 Planarity : 0.004 0.066 2229 Dihedral : 7.281 104.776 1973 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.19 % Allowed : 21.16 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1567 helix: 0.95 (0.19), residues: 709 sheet: -1.05 (0.40), residues: 178 loop : -1.68 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.002 0.000 HIS B 494 PHE 0.023 0.001 PHE A 774 TYR 0.012 0.001 TYR A 828 ARG 0.003 0.000 ARG B 265 Details of bonding type rmsd link_NAG-ASN : bond 0.00469 ( 10) link_NAG-ASN : angle 3.66665 ( 30) link_BETA1-4 : bond 0.00507 ( 4) link_BETA1-4 : angle 1.56413 ( 12) hydrogen bonds : bond 0.04334 ( 594) hydrogen bonds : angle 4.60228 ( 1722) SS BOND : bond 0.00246 ( 17) SS BOND : angle 0.86738 ( 34) covalent geometry : bond 0.00221 (12991) covalent geometry : angle 0.57459 (17641) *********************** 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 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 111 time to evaluate : 1.373 Fit side-chains REVERT: A 587 ASP cc_start: 0.8530 (p0) cc_final: 0.7944 (t0) REVERT: A 741 TRP cc_start: 0.7616 (OUTLIER) cc_final: 0.7108 (m100) REVERT: A 751 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7843 (mmm-85) REVERT: A 752 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 756 GLU cc_start: 0.7769 (tp30) cc_final: 0.7219 (tp30) REVERT: A 772 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8714 (pp) REVERT: A 845 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 462 HIS cc_start: 0.8586 (OUTLIER) cc_final: 0.8134 (m170) REVERT: B 725 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8015 (mt) REVERT: B 751 ARG cc_start: 0.9231 (mtp85) cc_final: 0.9003 (mtp85) outliers start: 43 outliers final: 17 residues processed: 142 average time/residue: 0.1996 time to fit residues: 45.2150 Evaluate side-chains 113 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 166 SER Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 772 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 394 CYS Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 725 LEU 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 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 80 optimal weight: 0.4980 chunk 148 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083879 restraints weight = 26669.388| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.91 r_work: 0.3231 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13022 Z= 0.153 Angle : 0.614 16.229 17717 Z= 0.297 Chirality : 0.047 0.682 2005 Planarity : 0.004 0.067 2229 Dihedral : 7.186 103.793 1973 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.23 % Allowed : 20.64 % Favored : 75.13 % 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: -0.44 (0.21), residues: 1567 helix: 1.05 (0.19), residues: 706 sheet: -0.93 (0.40), residues: 178 loop : -1.56 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.005 0.001 HIS A 462 PHE 0.022 0.001 PHE B 820 TYR 0.013 0.001 TYR A 824 ARG 0.002 0.000 ARG B 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00328 ( 10) link_NAG-ASN : angle 3.83149 ( 30) link_BETA1-4 : bond 0.00340 ( 4) link_BETA1-4 : angle 1.60286 ( 12) hydrogen bonds : bond 0.04658 ( 594) hydrogen bonds : angle 4.54008 ( 1722) SS BOND : bond 0.00398 ( 17) SS BOND : angle 1.03967 ( 34) covalent geometry : bond 0.00348 (12991) covalent geometry : angle 0.59148 (17641) *********************** 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 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 97 time to evaluate : 3.156 Fit side-chains REVERT: A 223 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 413 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8118 (mp) REVERT: A 587 ASP cc_start: 0.8467 (p0) cc_final: 0.7922 (t0) REVERT: A 741 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.7081 (m100) REVERT: A 751 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7890 (mmm-85) REVERT: A 752 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.6772 (p0) REVERT: A 756 GLU cc_start: 0.7811 (tp30) cc_final: 0.7264 (tp30) REVERT: A 772 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 845 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: B 307 MET cc_start: 0.8049 (mtp) cc_final: 0.7552 (mtt) REVERT: B 698 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7790 (p) outliers start: 57 outliers final: 34 residues processed: 140 average time/residue: 0.2018 time to fit residues: 47.2076 Evaluate side-chains 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 223 ILE 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 317 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE 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 725 LEU Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 751 ARG Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 772 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 602 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 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 851 ILE 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 61 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.124095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.082414 restraints weight = 26860.688| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.06 r_work: 0.3186 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13022 Z= 0.170 Angle : 0.628 17.398 17717 Z= 0.299 Chirality : 0.048 0.705 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.154 104.652 1973 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.86 % Allowed : 21.90 % Favored : 74.24 % 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: -0.36 (0.21), residues: 1567 helix: 1.10 (0.19), residues: 713 sheet: -0.96 (0.38), residues: 196 loop : -1.51 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.005 0.001 HIS A 462 PHE 0.028 0.001 PHE A 774 TYR 0.011 0.001 TYR A 824 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 10) link_NAG-ASN : angle 3.88459 ( 30) link_BETA1-4 : bond 0.00218 ( 4) link_BETA1-4 : angle 1.61254 ( 12) hydrogen bonds : bond 0.04612 ( 594) hydrogen bonds : angle 4.54727 ( 1722) SS BOND : bond 0.00329 ( 17) SS BOND : angle 1.06722 ( 34) covalent geometry : bond 0.00394 (12991) covalent geometry : angle 0.60538 (17641) *********************** 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 145 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 1.405 Fit side-chains REVERT: A 223 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7649 (tp) REVERT: A 587 ASP cc_start: 0.8552 (p0) cc_final: 0.8015 (t0) REVERT: A 751 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8141 (mmm-85) REVERT: A 756 GLU cc_start: 0.7839 (tp30) cc_final: 0.7294 (tp30) REVERT: A 814 PHE cc_start: 0.8179 (m-80) cc_final: 0.7907 (m-80) REVERT: A 845 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: B 307 MET cc_start: 0.8159 (mtp) cc_final: 0.7653 (mtt) REVERT: B 725 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7939 (mt) outliers start: 52 outliers final: 33 residues processed: 130 average time/residue: 0.1950 time to fit residues: 41.2861 Evaluate side-chains 125 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 88 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 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 433 ILE 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 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 751 ARG 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 437 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 696 VAL 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 832 VAL Chi-restraints excluded: chain B residue 833 SER 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 59 optimal weight: 20.0000 chunk 94 optimal weight: 0.0020 chunk 130 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 64 optimal weight: 40.0000 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- 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 335 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.124103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.082049 restraints weight = 26775.865| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.03 r_work: 0.3185 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13022 Z= 0.150 Angle : 0.624 16.294 17717 Z= 0.297 Chirality : 0.047 0.693 2005 Planarity : 0.004 0.071 2229 Dihedral : 7.130 104.407 1973 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.41 % Allowed : 22.64 % Favored : 73.94 % 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: -0.28 (0.21), residues: 1567 helix: 1.17 (0.19), residues: 710 sheet: -0.92 (0.38), residues: 196 loop : -1.46 (0.23), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.004 0.001 HIS A 462 PHE 0.015 0.001 PHE B 852 TYR 0.011 0.001 TYR B 824 ARG 0.004 0.000 ARG A 677 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 10) link_NAG-ASN : angle 3.82291 ( 30) link_BETA1-4 : bond 0.00221 ( 4) link_BETA1-4 : angle 1.63244 ( 12) hydrogen bonds : bond 0.04472 ( 594) hydrogen bonds : angle 4.48654 ( 1722) SS BOND : bond 0.00317 ( 17) SS BOND : angle 1.48948 ( 34) covalent geometry : bond 0.00341 (12991) covalent geometry : angle 0.59969 (17641) *********************** 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 138 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 1.538 Fit side-chains REVERT: A 587 ASP cc_start: 0.8486 (p0) cc_final: 0.7913 (t0) REVERT: A 751 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8164 (mmm-85) REVERT: A 756 GLU cc_start: 0.7884 (tp30) cc_final: 0.7361 (tp30) REVERT: A 814 PHE cc_start: 0.8161 (m-80) cc_final: 0.7841 (m-80) REVERT: A 845 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: B 307 MET cc_start: 0.8143 (mtp) cc_final: 0.7683 (mtt) REVERT: B 698 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8052 (p) REVERT: B 725 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7969 (mt) outliers start: 46 outliers final: 35 residues processed: 126 average time/residue: 0.1883 time to fit residues: 38.9862 Evaluate side-chains 129 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 466 LEU 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 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 751 ARG Chi-restraints excluded: chain A residue 760 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 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 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 92 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 335 GLN B 471 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.122722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.080579 restraints weight = 27033.800| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.04 r_work: 0.3149 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13022 Z= 0.213 Angle : 0.667 17.242 17717 Z= 0.322 Chirality : 0.049 0.714 2005 Planarity : 0.004 0.073 2229 Dihedral : 7.320 105.700 1973 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.41 % Allowed : 22.42 % Favored : 74.16 % 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: -0.33 (0.21), residues: 1567 helix: 1.15 (0.19), residues: 703 sheet: -1.05 (0.37), residues: 208 loop : -1.45 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 674 HIS 0.006 0.001 HIS A 462 PHE 0.018 0.001 PHE B 852 TYR 0.011 0.001 TYR B 417 ARG 0.003 0.000 ARG A 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 10) link_NAG-ASN : angle 3.99729 ( 30) link_BETA1-4 : bond 0.00180 ( 4) link_BETA1-4 : angle 1.68969 ( 12) hydrogen bonds : bond 0.04957 ( 594) hydrogen bonds : angle 4.58115 ( 1722) SS BOND : bond 0.00389 ( 17) SS BOND : angle 1.49482 ( 34) covalent geometry : bond 0.00501 (12991) covalent geometry : angle 0.64287 (17641) *********************** 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 133 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 87 time to evaluate : 1.494 Fit side-chains REVERT: A 587 ASP cc_start: 0.8578 (p0) cc_final: 0.7944 (t0) REVERT: A 751 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8124 (mmm-85) REVERT: A 756 GLU cc_start: 0.8011 (tp30) cc_final: 0.7391 (tp30) REVERT: A 814 PHE cc_start: 0.8065 (m-80) cc_final: 0.7733 (m-80) REVERT: A 845 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7553 (m-80) REVERT: B 307 MET cc_start: 0.8226 (mtp) cc_final: 0.7799 (mtt) REVERT: B 698 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8071 (p) REVERT: B 725 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8063 (mt) outliers start: 46 outliers final: 37 residues processed: 121 average time/residue: 0.2062 time to fit residues: 40.4572 Evaluate side-chains 123 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 466 LEU 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 615 LEU 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 755 LEU Chi-restraints excluded: chain A residue 760 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 317 THR Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 658 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 125 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 112 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.123607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082290 restraints weight = 26760.089| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.94 r_work: 0.3190 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.144 Angle : 0.625 16.936 17717 Z= 0.296 Chirality : 0.048 0.695 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.191 104.794 1973 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 23.01 % 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: -0.25 (0.21), residues: 1567 helix: 1.19 (0.19), residues: 707 sheet: -1.00 (0.37), residues: 208 loop : -1.39 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 299 HIS 0.004 0.001 HIS A 462 PHE 0.015 0.001 PHE B 604 TYR 0.012 0.001 TYR B 824 ARG 0.003 0.000 ARG B 751 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 10) link_NAG-ASN : angle 3.81361 ( 30) link_BETA1-4 : bond 0.00258 ( 4) link_BETA1-4 : angle 1.61603 ( 12) hydrogen bonds : bond 0.04490 ( 594) hydrogen bonds : angle 4.44470 ( 1722) SS BOND : bond 0.00322 ( 17) SS BOND : angle 1.22301 ( 34) covalent geometry : bond 0.00329 (12991) covalent geometry : angle 0.60272 (17641) *********************** 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 126 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 1.353 Fit side-chains REVERT: A 587 ASP cc_start: 0.8581 (p0) cc_final: 0.7948 (t0) REVERT: A 751 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7934 (mmm-85) REVERT: A 756 GLU cc_start: 0.8013 (tp30) cc_final: 0.7405 (tp30) REVERT: A 814 PHE cc_start: 0.8049 (m-80) cc_final: 0.7711 (m-80) REVERT: A 845 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: B 307 MET cc_start: 0.8149 (mtp) cc_final: 0.7690 (mtt) REVERT: B 698 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 725 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8052 (mt) outliers start: 40 outliers final: 30 residues processed: 117 average time/residue: 0.1870 time to fit residues: 35.3858 Evaluate side-chains 114 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 466 LEU 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 649 LEU Chi-restraints excluded: chain A residue 683 PHE 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 437 THR 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 68 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 100 optimal weight: 0.0270 chunk 71 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.124143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082838 restraints weight = 26575.977| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.96 r_work: 0.3158 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13022 Z= 0.150 Angle : 0.625 16.972 17717 Z= 0.297 Chirality : 0.048 0.689 2005 Planarity : 0.004 0.069 2229 Dihedral : 7.158 104.145 1973 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.97 % Allowed : 23.09 % Favored : 73.94 % 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: -0.17 (0.21), residues: 1567 helix: 1.24 (0.19), residues: 702 sheet: -1.03 (0.38), residues: 184 loop : -1.30 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 299 HIS 0.005 0.001 HIS A 462 PHE 0.020 0.001 PHE B 852 TYR 0.012 0.001 TYR B 824 ARG 0.007 0.000 ARG B 751 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 10) link_NAG-ASN : angle 3.78237 ( 30) link_BETA1-4 : bond 0.00202 ( 4) link_BETA1-4 : angle 1.62059 ( 12) hydrogen bonds : bond 0.04468 ( 594) hydrogen bonds : angle 4.41741 ( 1722) SS BOND : bond 0.00378 ( 17) SS BOND : angle 1.37959 ( 34) covalent geometry : bond 0.00344 (12991) covalent geometry : angle 0.60160 (17641) ********************** 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 125 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 1.520 Fit side-chains REVERT: A 231 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8030 (mm-30) REVERT: A 587 ASP cc_start: 0.8640 (p0) cc_final: 0.7952 (t0) REVERT: A 751 ARG cc_start: 0.8375 (mtp180) cc_final: 0.8063 (mmm-85) REVERT: A 756 GLU cc_start: 0.7986 (tp30) cc_final: 0.7248 (tp30) REVERT: A 810 MET cc_start: 0.6063 (mtm) cc_final: 0.5447 (ttt) REVERT: A 814 PHE cc_start: 0.8036 (m-80) cc_final: 0.7668 (m-80) REVERT: B 307 MET cc_start: 0.8164 (mtp) cc_final: 0.7685 (mtt) REVERT: B 698 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8250 (p) outliers start: 40 outliers final: 33 residues processed: 116 average time/residue: 0.2005 time to fit residues: 38.2600 Evaluate side-chains 119 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 433 ILE Chi-restraints excluded: chain A residue 466 LEU 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 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 760 ILE 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 437 THR 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 753 HIS Chi-restraints excluded: chain B residue 762 ILE 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 40 optimal weight: 0.0980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 100 optimal weight: 0.0030 chunk 80 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 638 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.126292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086288 restraints weight = 26233.258| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.94 r_work: 0.3231 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13022 Z= 0.110 Angle : 0.604 16.705 17717 Z= 0.284 Chirality : 0.046 0.670 2005 Planarity : 0.004 0.067 2229 Dihedral : 6.980 102.299 1973 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.82 % Allowed : 23.24 % Favored : 73.94 % 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: -0.07 (0.21), residues: 1567 helix: 1.29 (0.20), residues: 705 sheet: -0.93 (0.39), residues: 184 loop : -1.21 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 299 HIS 0.007 0.001 HIS A 462 PHE 0.015 0.001 PHE B 604 TYR 0.013 0.001 TYR A 824 ARG 0.007 0.000 ARG B 751 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 10) link_NAG-ASN : angle 3.62254 ( 30) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 1.57691 ( 12) hydrogen bonds : bond 0.04106 ( 594) hydrogen bonds : angle 4.33692 ( 1722) SS BOND : bond 0.00278 ( 17) SS BOND : angle 1.16264 ( 34) covalent geometry : bond 0.00238 (12991) covalent geometry : angle 0.58341 (17641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7503.42 seconds wall clock time: 130 minutes 0.11 seconds (7800.11 seconds total)