Starting phenix.real_space_refine on Fri Jul 3 07:17:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dd6_30645/07_2026/7dd6_30645.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1} 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: {'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 2.78, per 1000 atoms: 0.22 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: 1.17 Conformation dependent library (CDL) restraints added in 571.3 milliseconds 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: 0.39 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: 1.85 Time building geometry restraints manager: 1.53 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 - 17.99: 6707 17.99 - 35.99: 618 35.99 - 53.98: 158 53.98 - 71.97: 32 71.97 - 89.96: 20 Dihedral angle restraints: 7535 sinusoidal: 2931 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 7532 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 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 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: 1.560 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.100 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 15.529 89.962 4504 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG B 677 TYR 0.014 0.001 TYR A 750 PHE 0.015 0.001 PHE B 562 TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00829 / 0.43 (12991) covalent geometry : angle 0.80855 / 0.45 (17641) SS BOND : bond 0.27788 / 17.28 ( 17) SS BOND : angle 15.19897 / 10.56 ( 34) hydrogen bonds : bond 0.13911 / 8.75 ( 594) hydrogen bonds : angle 6.70983 / 4.67 ( 1722) link_BETA1-4 : bond 0.00479 / 0.24 ( 4) link_BETA1-4 : angle 1.05161 / 0.68 ( 12) link_NAG-ASN : bond 0.00406 / 0.28 ( 10) link_NAG-ASN : angle 3.51666 / 3.04 ( 30) *********************** 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 : 0.593 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: 0.7218 (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: 0.6537 (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: 0.8191 (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: 0.1140 time to fit residues: 32.2044 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 : 0.492 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 GLN A 335 GLN A 465 HIS ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 734 GLN B 799 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.125874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083855 restraints weight = 26832.867| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.25 r_work: 0.3171 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13022 Z= 0.166 Angle : 0.688 15.674 17717 Z= 0.344 Chirality : 0.049 0.576 2005 Planarity : 0.005 0.061 2229 Dihedral : 4.829 34.789 1681 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.27 % Allowed : 20.71 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.20), residues: 1567 helix: 0.07 (0.19), residues: 708 sheet: -1.60 (0.37), residues: 177 loop : -2.29 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 265 TYR 0.013 0.001 TYR B 651 PHE 0.044 0.002 PHE A 814 TRP 0.016 0.001 TRP B 674 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (12991) covalent geometry : angle 0.66772 / 0.34 (17641) SS BOND : bond 0.00399 / 0.22 ( 17) SS BOND : angle 1.51612 / 1.04 ( 34) hydrogen bonds : bond 0.05563 / 3.67 ( 594) hydrogen bonds : angle 5.16161 / 3.59 ( 1722) link_BETA1-4 : bond 0.00213 / 0.11 ( 4) link_BETA1-4 : angle 1.18400 / 0.74 ( 12) link_NAG-ASN : bond 0.00409 / 0.22 ( 10) link_NAG-ASN : angle 3.74177 / 3.27 ( 30) *********************** 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 159 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 528 LEU cc_start: 0.9097 (tp) cc_final: 0.8712 (tt) REVERT: A 587 ASP cc_start: 0.8826 (p0) cc_final: 0.8201 (t0) REVERT: A 641 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6199 (mt) REVERT: A 751 ARG cc_start: 0.7395 (ptm160) cc_final: 0.6426 (ptm160) REVERT: A 752 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8166 (t0) REVERT: A 756 GLU cc_start: 0.7969 (tp30) cc_final: 0.7266 (tp30) REVERT: A 810 MET cc_start: 0.5908 (mtm) cc_final: 0.5591 (mtm) REVERT: A 845 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7228 (m-80) REVERT: B 787 PHE cc_start: 0.8111 (t80) cc_final: 0.7820 (t80) outliers start: 44 outliers final: 19 residues processed: 148 average time/residue: 0.0912 time to fit residues: 21.7606 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 : 0.497 ------------------------------------------------------------------------------- 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 301 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 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 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 632 VAL 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 15 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 10 optimal weight: 0.0070 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4067 r_free = 0.4067 target = 0.125296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.083404 restraints weight = 27202.246| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.08 r_work: 0.3215 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13022 Z= 0.140 Angle : 0.621 15.268 17717 Z= 0.306 Chirality : 0.047 0.534 2005 Planarity : 0.004 0.066 2229 Dihedral : 4.469 22.889 1679 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.19 % Allowed : 20.34 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.20), residues: 1567 helix: 0.60 (0.19), residues: 708 sheet: -1.37 (0.37), residues: 189 loop : -2.00 (0.21), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 54 TYR 0.010 0.001 TYR B 417 PHE 0.020 0.001 PHE B 633 TRP 0.010 0.001 TRP A 299 HIS 0.006 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (12991) covalent geometry : angle 0.60233 / 0.30 (17641) SS BOND : bond 0.00308 / 0.15 ( 17) SS BOND : angle 1.10317 / 0.76 ( 34) hydrogen bonds : bond 0.04967 / 3.30 ( 594) hydrogen bonds : angle 4.86206 / 3.39 ( 1722) link_BETA1-4 : bond 0.00207 / 0.11 ( 4) link_BETA1-4 : angle 1.13136 / 0.67 ( 12) link_NAG-ASN : bond 0.00406 / 0.21 ( 10) link_NAG-ASN : angle 3.50480 / 3.12 ( 30) *********************** 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 147 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 587 ASP cc_start: 0.8506 (p0) cc_final: 0.7933 (t0) REVERT: A 641 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6442 (mt) REVERT: A 752 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.6873 (p0) REVERT: A 756 GLU cc_start: 0.7912 (tp30) cc_final: 0.7348 (tp30) REVERT: A 845 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: B 462 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8187 (m170) REVERT: B 604 PHE cc_start: 0.7435 (p90) cc_final: 0.7232 (p90) outliers start: 43 outliers final: 21 residues processed: 137 average time/residue: 0.0866 time to fit residues: 19.3092 Evaluate side-chains 116 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 166 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 425 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 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 851 ILE 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 48 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 147 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN A 752 ASN B 338 HIS ** 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 = 0.4080 r_free = 0.4080 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.083924 restraints weight = 27176.509| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.02 r_work: 0.3218 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2995 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= 0.133 Angle : 0.607 14.960 17717 Z= 0.294 Chirality : 0.047 0.520 2005 Planarity : 0.004 0.066 2229 Dihedral : 4.267 24.078 1679 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.49 % Allowed : 21.46 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1567 helix: 0.90 (0.19), residues: 709 sheet: -1.19 (0.38), residues: 194 loop : -1.77 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 265 TYR 0.011 0.001 TYR A 824 PHE 0.016 0.001 PHE B 633 TRP 0.009 0.001 TRP A 299 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (12991) covalent geometry : angle 0.58942 / 0.29 (17641) SS BOND : bond 0.00292 / 0.15 ( 17) SS BOND : angle 1.01015 / 0.72 ( 34) hydrogen bonds : bond 0.04637 / 3.07 ( 594) hydrogen bonds : angle 4.67249 / 3.25 ( 1722) link_BETA1-4 : bond 0.00214 / 0.11 ( 4) link_BETA1-4 : angle 1.11869 / 0.66 ( 12) link_NAG-ASN : bond 0.00395 / 0.21 ( 10) link_NAG-ASN : angle 3.42358 / 3.05 ( 30) *********************** 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 146 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 0.608 Fit side-chains REVERT: A 229 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 587 ASP cc_start: 0.8593 (p0) cc_final: 0.7982 (t0) REVERT: A 741 TRP cc_start: 0.7630 (OUTLIER) cc_final: 0.7117 (m100) REVERT: A 752 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7776 (t0) REVERT: A 756 GLU cc_start: 0.7879 (tp30) cc_final: 0.7257 (tp30) REVERT: A 845 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: B 307 MET cc_start: 0.8052 (mtp) cc_final: 0.7561 (mtt) REVERT: B 462 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.8344 (m-70) REVERT: B 725 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7986 (mt) REVERT: B 787 PHE cc_start: 0.8435 (t80) cc_final: 0.8231 (t80) outliers start: 47 outliers final: 23 residues processed: 138 average time/residue: 0.0847 time to fit residues: 19.3995 Evaluate side-chains 118 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 462 HIS Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 753 HIS Chi-restraints excluded: chain B residue 772 LEU Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 861 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 594 HIS A 752 ASN ** 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 = 0.4050 r_free = 0.4050 target = 0.123274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.081225 restraints weight = 27289.378| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.00 r_work: 0.3170 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13022 Z= 0.208 Angle : 0.643 16.063 17717 Z= 0.316 Chirality : 0.049 0.530 2005 Planarity : 0.004 0.068 2229 Dihedral : 4.341 25.450 1679 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.16 % Allowed : 21.53 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.21), residues: 1567 helix: 0.97 (0.19), residues: 706 sheet: -1.14 (0.38), residues: 194 loop : -1.70 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.011 0.001 TYR B 417 PHE 0.019 0.001 PHE B 820 TRP 0.011 0.001 TRP A 299 HIS 0.005 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (12991) covalent geometry : angle 0.62463 / 0.31 (17641) SS BOND : bond 0.00396 / 0.20 ( 17) SS BOND : angle 1.13391 / 0.81 ( 34) hydrogen bonds : bond 0.05005 / 3.36 ( 594) hydrogen bonds : angle 4.68992 / 3.26 ( 1722) link_BETA1-4 : bond 0.00153 / 0.08 ( 4) link_BETA1-4 : angle 1.18953 / 0.67 ( 12) link_NAG-ASN : bond 0.00350 / 0.20 ( 10) link_NAG-ASN : angle 3.61477 / 3.24 ( 30) *********************** 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: 56 poor density : 98 time to evaluate : 0.493 Fit side-chains REVERT: A 223 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8103 (tp) REVERT: A 587 ASP cc_start: 0.8523 (p0) cc_final: 0.7955 (t0) REVERT: A 741 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.7067 (m100) REVERT: A 751 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8087 (mmt90) REVERT: A 752 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.7993 (t0) REVERT: A 756 GLU cc_start: 0.7913 (tp30) cc_final: 0.7327 (tp30) REVERT: A 845 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: B 307 MET cc_start: 0.8178 (mtp) cc_final: 0.7688 (mtt) REVERT: B 725 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mt) outliers start: 56 outliers final: 35 residues processed: 141 average time/residue: 0.0838 time to fit residues: 19.2470 Evaluate side-chains 127 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 309 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 741 TRP Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 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 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 79 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 71 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 ASN B 335 GLN ** 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 = 0.4059 r_free = 0.4059 target = 0.123605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082027 restraints weight = 26720.275| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.99 r_work: 0.3178 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13022 Z= 0.170 Angle : 0.621 15.448 17717 Z= 0.302 Chirality : 0.048 0.522 2005 Planarity : 0.004 0.070 2229 Dihedral : 4.263 25.739 1679 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.93 % Allowed : 21.97 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1567 helix: 1.06 (0.19), residues: 710 sheet: -1.04 (0.38), residues: 194 loop : -1.63 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.011 0.001 TYR A 824 PHE 0.015 0.001 PHE B 852 TRP 0.010 0.001 TRP A 299 HIS 0.004 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12991) covalent geometry : angle 0.60270 / 0.30 (17641) SS BOND : bond 0.00326 / 0.15 ( 17) SS BOND : angle 1.02257 / 0.74 ( 34) hydrogen bonds : bond 0.04744 / 3.19 ( 594) hydrogen bonds : angle 4.60117 / 3.20 ( 1722) link_BETA1-4 : bond 0.00107 / 0.06 ( 4) link_BETA1-4 : angle 1.13747 / 0.67 ( 12) link_NAG-ASN : bond 0.00354 / 0.19 ( 10) link_NAG-ASN : angle 3.51213 / 3.15 ( 30) *********************** 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 146 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 93 time to evaluate : 0.477 Fit side-chains REVERT: A 223 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 587 ASP cc_start: 0.8550 (p0) cc_final: 0.8033 (t0) REVERT: A 741 TRP cc_start: 0.7545 (OUTLIER) cc_final: 0.7041 (m100) REVERT: A 751 ARG cc_start: 0.8540 (mtp180) cc_final: 0.8208 (mmt90) REVERT: A 752 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8097 (t0) REVERT: A 756 GLU cc_start: 0.7964 (tp30) cc_final: 0.7391 (tp30) REVERT: A 808 PHE cc_start: 0.8139 (m-80) cc_final: 0.7937 (m-80) REVERT: A 845 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 307 MET cc_start: 0.8132 (mtp) cc_final: 0.7649 (mtt) REVERT: B 698 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 725 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8047 (mt) outliers start: 53 outliers final: 38 residues processed: 133 average time/residue: 0.0818 time to fit residues: 17.8498 Evaluate side-chains 131 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 280 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 424 TYR Chi-restraints excluded: chain A residue 425 SER 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 741 TRP Chi-restraints excluded: chain A residue 752 ASN Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 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 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 835 VAL 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 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 752 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 = 0.4051 r_free = 0.4051 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.081167 restraints weight = 26932.449| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.04 r_work: 0.3179 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13022 Z= 0.184 Angle : 0.632 15.492 17717 Z= 0.305 Chirality : 0.049 0.521 2005 Planarity : 0.004 0.071 2229 Dihedral : 4.264 26.126 1679 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.86 % Allowed : 22.49 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.21), residues: 1567 helix: 1.12 (0.19), residues: 709 sheet: -1.24 (0.36), residues: 216 loop : -1.52 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 286 TYR 0.011 0.001 TYR B 417 PHE 0.018 0.001 PHE B 788 TRP 0.010 0.001 TRP A 299 HIS 0.006 0.001 HIS A 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (12991) covalent geometry : angle 0.61410 / 0.30 (17641) SS BOND : bond 0.00339 / 0.15 ( 17) SS BOND : angle 1.02902 / 0.73 ( 34) hydrogen bonds : bond 0.04754 / 3.20 ( 594) hydrogen bonds : angle 4.56161 / 3.18 ( 1722) link_BETA1-4 : bond 0.00152 / 0.08 ( 4) link_BETA1-4 : angle 1.16474 / 0.67 ( 12) link_NAG-ASN : bond 0.00356 / 0.20 ( 10) link_NAG-ASN : angle 3.51476 / 3.15 ( 30) *********************** 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 143 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 91 time to evaluate : 0.412 Fit side-chains REVERT: A 223 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7711 (tp) REVERT: A 587 ASP cc_start: 0.8608 (p0) cc_final: 0.8000 (t0) REVERT: A 741 TRP cc_start: 0.7579 (OUTLIER) cc_final: 0.7060 (m100) REVERT: A 751 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8192 (mmt90) REVERT: A 752 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.7800 (t0) REVERT: A 756 GLU cc_start: 0.8013 (tp30) cc_final: 0.7445 (tp30) REVERT: A 772 LEU cc_start: 0.8894 (pp) cc_final: 0.8689 (pp) REVERT: A 810 MET cc_start: 0.6423 (mtm) cc_final: 0.5582 (ttp) REVERT: A 814 PHE cc_start: 0.8064 (m-80) cc_final: 0.7486 (m-80) REVERT: A 845 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: B 307 MET cc_start: 0.8202 (mtp) cc_final: 0.7749 (mtt) REVERT: B 698 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8125 (p) REVERT: B 725 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7970 (mt) outliers start: 52 outliers final: 39 residues processed: 132 average time/residue: 0.0867 time to fit residues: 18.6558 Evaluate side-chains 133 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 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 741 TRP Chi-restraints excluded: chain A residue 752 ASN 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 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 ILE 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 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 VAL 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 56 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 752 ASN B 445 ASN 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 = 0.4020 r_free = 0.4020 target = 0.121499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.079351 restraints weight = 26850.597| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.98 r_work: 0.3154 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13022 Z= 0.258 Angle : 0.702 16.980 17717 Z= 0.341 Chirality : 0.051 0.539 2005 Planarity : 0.004 0.073 2229 Dihedral : 4.474 27.725 1679 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.23 % Allowed : 22.12 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.21), residues: 1567 helix: 1.07 (0.19), residues: 703 sheet: -1.05 (0.39), residues: 184 loop : -1.62 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 751 TYR 0.013 0.002 TYR B 203 PHE 0.016 0.001 PHE B 788 TRP 0.010 0.002 TRP B 674 HIS 0.004 0.001 HIS B 753 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.26 (12991) covalent geometry : angle 0.68051 / 0.34 (17641) SS BOND : bond 0.00397 / 0.18 ( 17) SS BOND : angle 1.90156 / 1.15 ( 34) hydrogen bonds : bond 0.05165 / 3.49 ( 594) hydrogen bonds : angle 4.67106 / 3.25 ( 1722) link_BETA1-4 : bond 0.00232 / 0.11 ( 4) link_BETA1-4 : angle 1.28241 / 0.72 ( 12) link_NAG-ASN : bond 0.00435 / 0.29 ( 10) link_NAG-ASN : angle 3.70417 / 3.32 ( 30) *********************** 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 146 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 89 time to evaluate : 0.505 Fit side-chains REVERT: A 528 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8669 (tt) REVERT: A 587 ASP cc_start: 0.8573 (p0) cc_final: 0.7917 (t0) REVERT: A 751 ARG cc_start: 0.8629 (mtp180) cc_final: 0.8337 (mmt90) REVERT: A 756 GLU cc_start: 0.8031 (tp30) cc_final: 0.7350 (tp30) REVERT: A 810 MET cc_start: 0.6349 (mtm) cc_final: 0.5511 (ttp) REVERT: A 814 PHE cc_start: 0.8036 (m-80) cc_final: 0.7599 (m-80) REVERT: A 845 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: B 307 MET cc_start: 0.8216 (mtp) cc_final: 0.7782 (mtt) REVERT: B 317 THR cc_start: 0.8506 (m) cc_final: 0.8222 (p) REVERT: B 698 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 725 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8003 (mt) outliers start: 57 outliers final: 43 residues processed: 135 average time/residue: 0.0842 time to fit residues: 18.5353 Evaluate side-chains 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 87 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 845 PHE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 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 832 VAL Chi-restraints excluded: chain B residue 833 SER Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 837 VAL 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 44 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 138 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 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 = 0.4054 r_free = 0.4054 target = 0.123358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.081528 restraints weight = 26756.230| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.03 r_work: 0.3149 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13022 Z= 0.165 Angle : 0.650 17.307 17717 Z= 0.311 Chirality : 0.048 0.516 2005 Planarity : 0.004 0.070 2229 Dihedral : 4.307 27.466 1679 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.41 % Allowed : 23.01 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1567 helix: 1.17 (0.19), residues: 704 sheet: -1.00 (0.39), residues: 184 loop : -1.52 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 751 TYR 0.011 0.001 TYR B 824 PHE 0.016 0.001 PHE B 788 TRP 0.012 0.001 TRP B 299 HIS 0.003 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (12991) covalent geometry : angle 0.63215 / 0.31 (17641) SS BOND : bond 0.00324 / 0.15 ( 17) SS BOND : angle 1.41295 / 0.87 ( 34) hydrogen bonds : bond 0.04661 / 3.14 ( 594) hydrogen bonds : angle 4.52848 / 3.15 ( 1722) link_BETA1-4 : bond 0.00154 / 0.08 ( 4) link_BETA1-4 : angle 1.16965 / 0.70 ( 12) link_NAG-ASN : bond 0.00345 / 0.17 ( 10) link_NAG-ASN : angle 3.45962 / 3.10 ( 30) *********************** 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 134 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 0.422 Fit side-chains REVERT: A 587 ASP cc_start: 0.8632 (p0) cc_final: 0.7968 (t0) REVERT: A 751 ARG cc_start: 0.8498 (mtp180) cc_final: 0.8205 (mmt90) REVERT: A 756 GLU cc_start: 0.8039 (tp30) cc_final: 0.7312 (tp30) REVERT: A 810 MET cc_start: 0.6440 (mtm) cc_final: 0.5637 (ttp) REVERT: A 814 PHE cc_start: 0.8019 (m-80) cc_final: 0.7549 (m-80) REVERT: A 845 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: B 307 MET cc_start: 0.8213 (mtp) cc_final: 0.7743 (mtt) REVERT: B 698 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8194 (p) REVERT: B 725 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7998 (mt) outliers start: 46 outliers final: 36 residues processed: 124 average time/residue: 0.0808 time to fit residues: 16.7180 Evaluate side-chains 126 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 424 TYR Chi-restraints excluded: chain A residue 425 SER 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 B residue 61 ILE Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 352 TRP Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 641 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 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 837 VAL 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 3 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4056 r_free = 0.4056 target = 0.124026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.082456 restraints weight = 26863.083| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.01 r_work: 0.3160 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4179 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= 0.139 Angle : 0.633 17.757 17717 Z= 0.301 Chirality : 0.047 0.500 2005 Planarity : 0.004 0.069 2229 Dihedral : 4.192 26.458 1679 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.90 % Allowed : 23.61 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.21), residues: 1567 helix: 1.20 (0.20), residues: 706 sheet: -0.94 (0.39), residues: 184 loop : -1.42 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 751 TYR 0.012 0.001 TYR A 824 PHE 0.024 0.001 PHE B 618 TRP 0.012 0.001 TRP B 299 HIS 0.002 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12991) covalent geometry : angle 0.61638 / 0.30 (17641) SS BOND : bond 0.00311 / 0.15 ( 17) SS BOND : angle 1.25669 / 0.76 ( 34) hydrogen bonds : bond 0.04440 / 2.99 ( 594) hydrogen bonds : angle 4.46604 / 3.13 ( 1722) link_BETA1-4 : bond 0.00171 / 0.09 ( 4) link_BETA1-4 : angle 1.16323 / 0.68 ( 12) link_NAG-ASN : bond 0.00376 / 0.19 ( 10) link_NAG-ASN : angle 3.32871 / 2.97 ( 30) ********************** 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 124 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 85 time to evaluate : 0.480 Fit side-chains REVERT: A 587 ASP cc_start: 0.8637 (p0) cc_final: 0.7961 (t0) REVERT: A 751 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8196 (mmt90) REVERT: A 756 GLU cc_start: 0.7972 (tp30) cc_final: 0.7244 (tp30) REVERT: A 810 MET cc_start: 0.6384 (mtm) cc_final: 0.5599 (ttp) REVERT: A 814 PHE cc_start: 0.8009 (m-80) cc_final: 0.7529 (m-80) REVERT: B 307 MET cc_start: 0.8199 (mtp) cc_final: 0.7723 (mtt) REVERT: B 698 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8205 (p) REVERT: B 725 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8015 (mt) outliers start: 39 outliers final: 31 residues processed: 116 average time/residue: 0.0765 time to fit residues: 14.6842 Evaluate side-chains 116 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 78 ILE 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 424 TYR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 496 SER 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 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 641 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN A 638 ASN ** 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 = 0.4076 r_free = 0.4076 target = 0.124820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.083348 restraints weight = 26600.726| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.06 r_work: 0.3227 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4282 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= 0.124 Angle : 0.616 15.896 17717 Z= 0.292 Chirality : 0.047 0.487 2005 Planarity : 0.004 0.067 2229 Dihedral : 4.083 25.447 1679 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.67 % Allowed : 23.76 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.21), residues: 1567 helix: 1.26 (0.20), residues: 705 sheet: -0.88 (0.40), residues: 174 loop : -1.33 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 751 TYR 0.012 0.001 TYR A 824 PHE 0.024 0.001 PHE B 618 TRP 0.012 0.001 TRP B 299 HIS 0.002 0.000 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12991) covalent geometry : angle 0.60021 / 0.29 (17641) SS BOND : bond 0.00281 / 0.14 ( 17) SS BOND : angle 1.17286 / 0.71 ( 34) hydrogen bonds : bond 0.04250 / 2.86 ( 594) hydrogen bonds : angle 4.39351 / 3.07 ( 1722) link_BETA1-4 : bond 0.00200 / 0.10 ( 4) link_BETA1-4 : angle 1.12974 / 0.67 ( 12) link_NAG-ASN : bond 0.00403 / 0.20 ( 10) link_NAG-ASN : angle 3.23703 / 2.89 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.17 seconds wall clock time: 60 minutes 25.85 seconds (3625.85 seconds total)