Starting phenix.real_space_refine on Thu Dec 26 14:30:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.map" model { file = "/net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2g_43747/12_2024/8w2g_43747.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.335 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 148 5.16 5 C 14388 2.51 5 N 4068 2.21 5 O 4452 1.98 5 H 22628 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 1.83s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45720 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11313 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain: "D" Number of atoms: 11313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11313 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain: "B" Number of atoms: 11313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11313 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain: "C" Number of atoms: 11313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 11313 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'F6P': 1, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'F6P': 1, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'F6P': 1, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'ADP': 3, 'F6P': 1, 'FBP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1' ADP A 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP A 802 " occ=0.50 residue: pdb=" C1' ADP D 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP D 802 " occ=0.50 residue: pdb=" C1' ADP B 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP B 802 " occ=0.50 residue: pdb=" C1' ADP C 802 " occ=0.50 ... (25 atoms not shown) pdb=" PB ADP C 802 " occ=0.50 Time building chain proxies: 21.75, per 1000 atoms: 0.48 Number of scatterers: 45720 At special positions: 0 Unit cell: (159.327, 130.665, 128.979, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 36 15.00 O 4452 8.00 N 4068 7.00 C 14388 6.00 H 22628 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 11.26 Conformation dependent library (CDL) restraints added in 3.6 seconds 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5288 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 24 sheets defined 52.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.12 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 90 through 93 Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 118 through 142 removed outlier: 3.575A pdb=" N GLU A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY A 133 " --> pdb=" O ARG A 129 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 177 through 200 removed outlier: 4.054A pdb=" N THR A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 238 through 253 removed outlier: 3.973A pdb=" N PHE A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.500A pdb=" N GLN A 300 " --> pdb=" O GLY A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 366 through 375 Processing helix chain 'A' and resid 375 through 390 removed outlier: 4.334A pdb=" N GLU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 437 through 444 Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.682A pdb=" N VAL A 455 " --> pdb=" O TRP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.927A pdb=" N GLY A 460 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 475 removed outlier: 4.134A pdb=" N GLY A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 577 through 587 Processing helix chain 'A' and resid 600 through 615 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 668 through 693 Processing helix chain 'A' and resid 703 through 705 No H-bonds generated for 'chain 'A' and resid 703 through 705' Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.772A pdb=" N LYS A 727 " --> pdb=" O GLU A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 742 removed outlier: 3.802A pdb=" N LEU A 742 " --> pdb=" O GLN A 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 739 through 742' Processing helix chain 'A' and resid 743 through 752 removed outlier: 4.113A pdb=" N MET A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 94 through 108 Processing helix chain 'D' and resid 118 through 142 removed outlier: 3.571A pdb=" N GLU D 131 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLY D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 177 through 200 removed outlier: 4.052A pdb=" N THR D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 238 through 253 removed outlier: 3.974A pdb=" N PHE D 242 " --> pdb=" O GLY D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 297 through 300 removed outlier: 3.503A pdb=" N GLN D 300 " --> pdb=" O GLY D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 306 through 327 Processing helix chain 'D' and resid 348 through 364 Processing helix chain 'D' and resid 366 through 375 Processing helix chain 'D' and resid 375 through 390 removed outlier: 4.337A pdb=" N GLU D 379 " --> pdb=" O GLY D 375 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 Processing helix chain 'D' and resid 437 through 444 Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.682A pdb=" N VAL D 455 " --> pdb=" O TRP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 461 removed outlier: 3.929A pdb=" N GLY D 460 " --> pdb=" O GLY D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 475 removed outlier: 4.139A pdb=" N GLY D 475 " --> pdb=" O LEU D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 475' Processing helix chain 'D' and resid 476 through 487 Processing helix chain 'D' and resid 497 through 510 Processing helix chain 'D' and resid 540 through 562 Processing helix chain 'D' and resid 577 through 587 Processing helix chain 'D' and resid 600 through 615 Processing helix chain 'D' and resid 635 through 647 Processing helix chain 'D' and resid 659 through 664 Processing helix chain 'D' and resid 668 through 693 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.770A pdb=" N LYS D 727 " --> pdb=" O GLU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 742 removed outlier: 3.803A pdb=" N LEU D 742 " --> pdb=" O GLN D 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 739 through 742' Processing helix chain 'D' and resid 743 through 752 removed outlier: 4.112A pdb=" N MET D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 90 through 93 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 118 through 142 removed outlier: 3.572A pdb=" N GLU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N GLY B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'B' and resid 177 through 200 removed outlier: 4.056A pdb=" N THR B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 238 through 253 removed outlier: 3.972A pdb=" N PHE B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 288 Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.502A pdb=" N GLN B 300 " --> pdb=" O GLY B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 306 through 327 Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 375 through 390 removed outlier: 4.338A pdb=" N GLU B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 437 through 444 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.681A pdb=" N VAL B 455 " --> pdb=" O TRP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.932A pdb=" N GLY B 460 " --> pdb=" O GLY B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 475 removed outlier: 4.138A pdb=" N GLY B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 475' Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 497 through 510 Processing helix chain 'B' and resid 540 through 562 Processing helix chain 'B' and resid 577 through 587 Processing helix chain 'B' and resid 600 through 615 Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 668 through 693 Processing helix chain 'B' and resid 703 through 705 No H-bonds generated for 'chain 'B' and resid 703 through 705' Processing helix chain 'B' and resid 723 through 727 removed outlier: 3.768A pdb=" N LYS B 727 " --> pdb=" O GLU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 742 removed outlier: 3.800A pdb=" N LEU B 742 " --> pdb=" O GLN B 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 739 through 742' Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.112A pdb=" N MET B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 90 through 93 Processing helix chain 'C' and resid 94 through 108 Processing helix chain 'C' and resid 118 through 142 removed outlier: 3.575A pdb=" N GLU C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 177 through 200 removed outlier: 4.058A pdb=" N THR C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.973A pdb=" N PHE C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 Processing helix chain 'C' and resid 297 through 300 Processing helix chain 'C' and resid 306 through 327 Processing helix chain 'C' and resid 348 through 364 Processing helix chain 'C' and resid 366 through 375 Processing helix chain 'C' and resid 375 through 390 removed outlier: 4.332A pdb=" N GLU C 379 " --> pdb=" O GLY C 375 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N HIS C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 Processing helix chain 'C' and resid 437 through 444 Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.682A pdb=" N VAL C 455 " --> pdb=" O TRP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 461 removed outlier: 3.928A pdb=" N GLY C 460 " --> pdb=" O GLY C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 475 removed outlier: 4.134A pdb=" N GLY C 475 " --> pdb=" O LEU C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 475' Processing helix chain 'C' and resid 476 through 487 Processing helix chain 'C' and resid 497 through 510 Processing helix chain 'C' and resid 540 through 562 Processing helix chain 'C' and resid 577 through 587 Processing helix chain 'C' and resid 600 through 615 Processing helix chain 'C' and resid 635 through 647 Processing helix chain 'C' and resid 659 through 664 Processing helix chain 'C' and resid 668 through 693 Processing helix chain 'C' and resid 703 through 705 No H-bonds generated for 'chain 'C' and resid 703 through 705' Processing helix chain 'C' and resid 723 through 727 removed outlier: 3.772A pdb=" N LYS C 727 " --> pdb=" O GLU C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 742 removed outlier: 3.800A pdb=" N LEU C 742 " --> pdb=" O GLN C 739 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 739 through 742' Processing helix chain 'C' and resid 743 through 752 removed outlier: 4.113A pdb=" N MET C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 67 removed outlier: 4.918A pdb=" N THR A 22 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 17 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N CYS A 114 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY A 19 " --> pdb=" O CYS A 114 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 116 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 21 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 113 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU A 161 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 115 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 334 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.299A pdb=" N TRP A 227 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ALA A 263 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE A 229 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 447 through 449 removed outlier: 6.203A pdb=" N LEU A 402 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL A 435 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 404 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 401 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU A 493 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA A 403 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL A 495 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 405 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET A 521 " --> pdb=" O CYS A 708 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 710 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 523 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU A 712 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 593 removed outlier: 6.226A pdb=" N ALA A 591 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN A 627 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 593 " --> pdb=" O ASN A 627 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG A 565 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL A 624 " --> pdb=" O ARG A 565 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE A 567 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ARG A 626 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A 569 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL A 566 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN A 656 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 568 " --> pdb=" O ASN A 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AA6, first strand: chain 'A' and resid 729 through 730 Processing sheet with id=AA7, first strand: chain 'D' and resid 65 through 67 removed outlier: 4.919A pdb=" N THR D 22 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA D 17 " --> pdb=" O ASN D 112 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N CYS D 114 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY D 19 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE D 116 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 21 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 113 " --> pdb=" O ALA D 159 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU D 161 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL D 115 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS D 334 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.302A pdb=" N TRP D 227 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ALA D 263 " --> pdb=" O TRP D 227 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE D 229 " --> pdb=" O ALA D 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 447 through 449 removed outlier: 6.208A pdb=" N LEU D 402 " --> pdb=" O TYR D 433 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL D 435 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE D 404 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER D 401 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LEU D 493 " --> pdb=" O SER D 401 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA D 403 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL D 495 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU D 405 " --> pdb=" O VAL D 495 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET D 521 " --> pdb=" O CYS D 708 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE D 710 " --> pdb=" O MET D 521 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL D 523 " --> pdb=" O ILE D 710 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LEU D 712 " --> pdb=" O VAL D 523 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 591 through 593 removed outlier: 6.227A pdb=" N ALA D 591 " --> pdb=" O LEU D 625 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ASN D 627 " --> pdb=" O ALA D 591 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR D 593 " --> pdb=" O ASN D 627 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG D 565 " --> pdb=" O GLY D 622 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL D 624 " --> pdb=" O ARG D 565 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE D 567 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ARG D 626 " --> pdb=" O PHE D 567 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 569 " --> pdb=" O ARG D 626 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 566 " --> pdb=" O ARG D 654 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ASN D 656 " --> pdb=" O VAL D 566 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE D 568 " --> pdb=" O ASN D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 694 through 695 Processing sheet with id=AB3, first strand: chain 'D' and resid 729 through 730 Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 67 removed outlier: 4.919A pdb=" N THR B 22 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA B 17 " --> pdb=" O ASN B 112 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N CYS B 114 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY B 19 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 116 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 21 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 113 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU B 161 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 115 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS B 334 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.299A pdb=" N TRP B 227 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ALA B 263 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 229 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 202 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR B 294 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL B 204 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 447 through 449 removed outlier: 6.204A pdb=" N LEU B 402 " --> pdb=" O TYR B 433 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 435 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 404 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER B 401 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU B 493 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 403 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 495 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B 405 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET B 521 " --> pdb=" O CYS B 708 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE B 710 " --> pdb=" O MET B 521 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 523 " --> pdb=" O ILE B 710 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU B 712 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.225A pdb=" N ALA B 591 " --> pdb=" O LEU B 625 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN B 627 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR B 593 " --> pdb=" O ASN B 627 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ARG B 565 " --> pdb=" O GLY B 622 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL B 624 " --> pdb=" O ARG B 565 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE B 567 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG B 626 " --> pdb=" O PHE B 567 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 569 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 566 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN B 656 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE B 568 " --> pdb=" O ASN B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 694 through 695 Processing sheet with id=AB9, first strand: chain 'B' and resid 729 through 730 Processing sheet with id=AC1, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.918A pdb=" N THR C 22 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA C 17 " --> pdb=" O ASN C 112 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N CYS C 114 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY C 19 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE C 116 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 21 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 113 " --> pdb=" O ALA C 159 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL C 115 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS C 334 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 227 through 229 removed outlier: 6.295A pdb=" N TRP C 227 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ALA C 263 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE C 229 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 202 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N THR C 294 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 204 " --> pdb=" O THR C 294 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 447 through 449 removed outlier: 6.202A pdb=" N LEU C 402 " --> pdb=" O TYR C 433 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL C 435 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 404 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 401 " --> pdb=" O ALA C 491 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU C 493 " --> pdb=" O SER C 401 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 403 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL C 495 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU C 405 " --> pdb=" O VAL C 495 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET C 521 " --> pdb=" O CYS C 708 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE C 710 " --> pdb=" O MET C 521 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL C 523 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU C 712 " --> pdb=" O VAL C 523 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 591 through 593 removed outlier: 6.227A pdb=" N ALA C 591 " --> pdb=" O LEU C 625 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ASN C 627 " --> pdb=" O ALA C 591 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR C 593 " --> pdb=" O ASN C 627 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 565 " --> pdb=" O GLY C 622 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL C 624 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE C 567 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ARG C 626 " --> pdb=" O PHE C 567 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 569 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 566 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN C 656 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE C 568 " --> pdb=" O ASN C 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 694 through 695 Processing sheet with id=AC6, first strand: chain 'C' and resid 729 through 730 1177 hydrogen bonds defined for protein. 3408 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: 20.91 Time building geometry restraints manager: 13.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22572 1.03 - 1.23: 72 1.23 - 1.42: 9724 1.42 - 1.62: 13472 1.62 - 1.82: 308 Bond restraints: 46148 Sorted by residual: bond pdb=" C5 FBP B 805 " pdb=" O5 FBP B 805 " ideal model delta sigma weight residual 1.608 1.278 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb=" C5 FBP C 805 " pdb=" O5 FBP C 805 " ideal model delta sigma weight residual 1.608 1.280 0.328 2.00e-02 2.50e+03 2.68e+02 bond pdb=" C5 FBP A 805 " pdb=" O5 FBP A 805 " ideal model delta sigma weight residual 1.608 1.281 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C5 FBP D 805 " pdb=" O5 FBP D 805 " ideal model delta sigma weight residual 1.608 1.281 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C4 FBP C 805 " pdb=" C5 FBP C 805 " ideal model delta sigma weight residual 1.346 1.665 -0.319 2.00e-02 2.50e+03 2.54e+02 ... (remaining 46143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 81330 2.23 - 4.46: 1604 4.46 - 6.69: 162 6.69 - 8.92: 20 8.92 - 11.15: 48 Bond angle restraints: 83164 Sorted by residual: angle pdb=" O1A ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sigma weight residual 119.90 108.75 11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1A ADP B 802 " pdb=" PA ADP B 802 " pdb=" O2A ADP B 802 " ideal model delta sigma weight residual 119.90 108.75 11.15 3.00e+00 1.11e-01 1.38e+01 angle pdb=" O1A ADP A 802 " pdb=" PA ADP A 802 " pdb=" O2A ADP A 802 " ideal model delta sigma weight residual 119.90 108.84 11.06 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1A ADP C 802 " pdb=" PA ADP C 802 " pdb=" O2A ADP C 802 " ideal model delta sigma weight residual 119.90 108.85 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O1B ADP C 804 " pdb=" PB ADP C 804 " pdb=" O2B ADP C 804 " ideal model delta sigma weight residual 119.90 109.28 10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 83159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 20747 33.23 - 66.46: 799 66.46 - 99.69: 84 99.69 - 132.92: 8 132.92 - 166.15: 10 Dihedral angle restraints: 21648 sinusoidal: 12056 harmonic: 9592 Sorted by residual: dihedral pdb=" O1B ADP A 804 " pdb=" O3A ADP A 804 " pdb=" PB ADP A 804 " pdb=" PA ADP A 804 " ideal model delta sinusoidal sigma weight residual 300.00 133.85 166.15 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP D 804 " pdb=" O3A ADP D 804 " pdb=" PB ADP D 804 " pdb=" PA ADP D 804 " ideal model delta sinusoidal sigma weight residual 300.00 141.43 158.57 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C5' ADP C 804 " pdb=" O5' ADP C 804 " pdb=" PA ADP C 804 " pdb=" O2A ADP C 804 " ideal model delta sinusoidal sigma weight residual 300.00 147.95 152.05 1 2.00e+01 2.50e-03 4.52e+01 ... (remaining 21645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2566 0.043 - 0.085: 730 0.085 - 0.128: 214 0.128 - 0.171: 65 0.171 - 0.214: 5 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CB VAL A 455 " pdb=" CA VAL A 455 " pdb=" CG1 VAL A 455 " pdb=" CG2 VAL A 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL D 455 " pdb=" CA VAL D 455 " pdb=" CG1 VAL D 455 " pdb=" CG2 VAL D 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL B 455 " pdb=" CA VAL B 455 " pdb=" CG1 VAL B 455 " pdb=" CG2 VAL B 455 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3577 not shown) Planarity restraints: 6920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 346 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO C 347 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 735 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO C 736 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 736 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 736 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 735 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 736 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 736 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 736 " -0.019 5.00e-02 4.00e+02 ... (remaining 6917 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 6542 2.28 - 2.86: 104315 2.86 - 3.44: 121681 3.44 - 4.02: 172354 4.02 - 4.60: 263965 Nonbonded interactions: 668857 Sorted by model distance: nonbonded pdb=" O GLN D 200 " pdb="HH21 ARG D 251 " model vdw 1.700 2.450 nonbonded pdb=" O GLN B 200 " pdb="HH21 ARG B 251 " model vdw 1.701 2.450 nonbonded pdb=" O GLN A 200 " pdb="HH21 ARG A 251 " model vdw 1.702 2.450 nonbonded pdb=" O GLN C 200 " pdb="HH21 ARG C 251 " model vdw 1.703 2.450 nonbonded pdb=" HG1 THR B 543 " pdb=" OD2 ASP B 671 " model vdw 1.707 2.450 ... (remaining 668852 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.50 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: 4.430 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: 0.780 Extract box with map and model: 1.580 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 95.340 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.014 0.330 23520 Z= 0.931 Angle : 0.873 11.149 31892 Z= 0.406 Chirality : 0.046 0.214 3580 Planarity : 0.004 0.038 4040 Dihedral : 16.266 166.147 8756 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 2956 helix: 0.12 (0.12), residues: 1484 sheet: -0.41 (0.21), residues: 468 loop : -0.94 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 741 HIS 0.006 0.001 HIS A 211 PHE 0.012 0.002 PHE A 439 TYR 0.014 0.002 TYR C 674 ARG 0.010 0.001 ARG D 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 673 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8014 (m-80) cc_final: 0.7709 (m-80) REVERT: A 90 LYS cc_start: 0.7505 (tppp) cc_final: 0.7237 (tmmt) REVERT: A 190 ASP cc_start: 0.7968 (m-30) cc_final: 0.7617 (m-30) REVERT: A 379 GLU cc_start: 0.7269 (tp30) cc_final: 0.6746 (tm-30) REVERT: A 383 ASN cc_start: 0.7370 (m-40) cc_final: 0.7033 (m110) REVERT: D 55 TYR cc_start: 0.8010 (m-80) cc_final: 0.7711 (m-80) REVERT: D 90 LYS cc_start: 0.7522 (tppp) cc_final: 0.7272 (tmmt) REVERT: D 190 ASP cc_start: 0.7955 (m-30) cc_final: 0.7612 (m-30) REVERT: B 55 TYR cc_start: 0.8017 (m-80) cc_final: 0.7710 (m-80) REVERT: B 90 LYS cc_start: 0.7517 (tppp) cc_final: 0.7276 (tmmt) REVERT: B 190 ASP cc_start: 0.7904 (m-30) cc_final: 0.7553 (m-30) REVERT: B 379 GLU cc_start: 0.7301 (tp30) cc_final: 0.6897 (tm-30) REVERT: B 383 ASN cc_start: 0.7343 (m-40) cc_final: 0.7092 (m110) REVERT: C 90 LYS cc_start: 0.7520 (tppp) cc_final: 0.7257 (tmmt) REVERT: C 190 ASP cc_start: 0.7922 (m-30) cc_final: 0.7587 (m-30) REVERT: C 383 ASN cc_start: 0.7382 (m-40) cc_final: 0.7114 (m-40) outliers start: 0 outliers final: 0 residues processed: 673 average time/residue: 2.4068 time to fit residues: 1922.9264 Evaluate side-chains 500 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 232 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 268 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 353 GLN A 448 GLN D 75 ASN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN B 75 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 75 ASN C 353 GLN C 448 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23520 Z= 0.197 Angle : 0.654 7.091 31892 Z= 0.313 Chirality : 0.042 0.157 3580 Planarity : 0.004 0.044 4040 Dihedral : 13.120 150.673 3568 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.01 % Allowed : 12.84 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2956 helix: 1.60 (0.13), residues: 1468 sheet: -0.15 (0.22), residues: 476 loop : -0.69 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 382 HIS 0.003 0.001 HIS A 108 PHE 0.013 0.001 PHE C 378 TYR 0.013 0.001 TYR C 674 ARG 0.004 0.000 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 503 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8076 (m-80) cc_final: 0.7740 (m-80) REVERT: A 88 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6746 (mtm-85) REVERT: A 190 ASP cc_start: 0.7809 (m-30) cc_final: 0.7601 (m-30) REVERT: A 210 ARG cc_start: 0.7066 (ttt-90) cc_final: 0.6833 (mtp-110) REVERT: A 727 LYS cc_start: 0.8291 (mttp) cc_final: 0.8018 (ptpt) REVERT: D 55 TYR cc_start: 0.8080 (m-80) cc_final: 0.7758 (m-80) REVERT: D 88 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6660 (mtm-85) REVERT: D 190 ASP cc_start: 0.7781 (m-30) cc_final: 0.7570 (m-30) REVERT: B 55 TYR cc_start: 0.8081 (m-80) cc_final: 0.7755 (m-80) REVERT: B 88 ARG cc_start: 0.6993 (ttm110) cc_final: 0.6740 (mtm-85) REVERT: B 190 ASP cc_start: 0.7785 (m-30) cc_final: 0.7577 (m-30) REVERT: B 683 MET cc_start: 0.8469 (tpp) cc_final: 0.7989 (tpt) REVERT: C 55 TYR cc_start: 0.7986 (m-80) cc_final: 0.7685 (m-80) REVERT: C 88 ARG cc_start: 0.7013 (ttm110) cc_final: 0.6729 (mtm-85) REVERT: C 190 ASP cc_start: 0.7797 (m-30) cc_final: 0.7591 (m-30) outliers start: 24 outliers final: 7 residues processed: 521 average time/residue: 2.3663 time to fit residues: 1468.9450 Evaluate side-chains 484 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 477 time to evaluate : 3.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23520 Z= 0.283 Angle : 0.657 7.019 31892 Z= 0.312 Chirality : 0.043 0.162 3580 Planarity : 0.003 0.034 4040 Dihedral : 12.332 144.071 3568 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.05 % Allowed : 14.56 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.15), residues: 2956 helix: 1.84 (0.13), residues: 1488 sheet: -0.08 (0.22), residues: 496 loop : -0.72 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 382 HIS 0.003 0.001 HIS B 660 PHE 0.010 0.001 PHE C 308 TYR 0.014 0.001 TYR C 43 ARG 0.005 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 472 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8118 (m-80) cc_final: 0.7736 (m-80) REVERT: A 88 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6770 (mtm-85) REVERT: A 190 ASP cc_start: 0.8032 (m-30) cc_final: 0.7700 (m-30) REVERT: A 210 ARG cc_start: 0.7094 (ttt-90) cc_final: 0.6884 (mtp-110) REVERT: D 55 TYR cc_start: 0.8126 (m-80) cc_final: 0.7740 (m-80) REVERT: D 88 ARG cc_start: 0.7055 (ttm170) cc_final: 0.6817 (mtm-85) REVERT: D 190 ASP cc_start: 0.8034 (m-30) cc_final: 0.7692 (m-30) REVERT: D 210 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6811 (mtp-110) REVERT: B 55 TYR cc_start: 0.8128 (m-80) cc_final: 0.7758 (m-80) REVERT: B 88 ARG cc_start: 0.7061 (ttm170) cc_final: 0.6803 (mtm-85) REVERT: B 190 ASP cc_start: 0.8131 (m-30) cc_final: 0.7802 (m-30) REVERT: B 210 ARG cc_start: 0.7132 (mtp85) cc_final: 0.6785 (mtp-110) REVERT: C 55 TYR cc_start: 0.8031 (m-80) cc_final: 0.7649 (m-80) REVERT: C 88 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6760 (mtm-85) REVERT: C 190 ASP cc_start: 0.8041 (m-30) cc_final: 0.7706 (m-30) outliers start: 25 outliers final: 23 residues processed: 484 average time/residue: 2.4287 time to fit residues: 1397.3179 Evaluate side-chains 474 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 451 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23520 Z= 0.301 Angle : 0.661 6.994 31892 Z= 0.315 Chirality : 0.043 0.162 3580 Planarity : 0.003 0.035 4040 Dihedral : 11.339 137.406 3568 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.43 % Allowed : 14.93 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 2956 helix: 1.87 (0.13), residues: 1492 sheet: 0.00 (0.22), residues: 500 loop : -0.74 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 382 HIS 0.002 0.001 HIS B 733 PHE 0.015 0.002 PHE B 378 TYR 0.023 0.002 TYR A 103 ARG 0.006 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 474 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8110 (m-80) cc_final: 0.7738 (m-80) REVERT: A 88 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6682 (mtm-85) REVERT: A 190 ASP cc_start: 0.8192 (m-30) cc_final: 0.7895 (m-30) REVERT: A 365 LYS cc_start: 0.7837 (mptt) cc_final: 0.7522 (mppt) REVERT: D 55 TYR cc_start: 0.8118 (m-80) cc_final: 0.7747 (m-80) REVERT: D 88 ARG cc_start: 0.6997 (ttm170) cc_final: 0.6663 (mtm-85) REVERT: D 190 ASP cc_start: 0.8163 (m-30) cc_final: 0.7876 (m-30) REVERT: D 210 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6871 (mtp-110) REVERT: D 365 LYS cc_start: 0.7841 (mptt) cc_final: 0.7519 (mppt) REVERT: B 55 TYR cc_start: 0.8120 (m-80) cc_final: 0.7754 (m-80) REVERT: B 88 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6753 (mtm-85) REVERT: B 190 ASP cc_start: 0.8165 (m-30) cc_final: 0.7874 (m-30) REVERT: B 210 ARG cc_start: 0.7176 (mtp85) cc_final: 0.6860 (mtp-110) REVERT: B 365 LYS cc_start: 0.7843 (mptt) cc_final: 0.7523 (mppt) REVERT: C 55 TYR cc_start: 0.8057 (m-80) cc_final: 0.7848 (m-80) REVERT: C 88 ARG cc_start: 0.7039 (ttm170) cc_final: 0.6665 (mtm-85) REVERT: C 190 ASP cc_start: 0.8203 (m-30) cc_final: 0.7903 (m-30) REVERT: C 365 LYS cc_start: 0.7825 (mptt) cc_final: 0.7476 (mppt) outliers start: 34 outliers final: 32 residues processed: 489 average time/residue: 2.4326 time to fit residues: 1414.1252 Evaluate side-chains 497 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 465 time to evaluate : 3.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 618 ASP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 618 ASP Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 72 optimal weight: 0.0870 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23520 Z= 0.189 Angle : 0.615 7.045 31892 Z= 0.288 Chirality : 0.041 0.150 3580 Planarity : 0.003 0.040 4040 Dihedral : 10.802 134.656 3568 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.01 % Allowed : 16.53 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.16), residues: 2956 helix: 2.13 (0.14), residues: 1492 sheet: 0.04 (0.23), residues: 496 loop : -0.59 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 382 HIS 0.005 0.001 HIS B 390 PHE 0.009 0.001 PHE A 308 TYR 0.022 0.001 TYR C 103 ARG 0.005 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 474 time to evaluate : 3.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8099 (m-80) cc_final: 0.7750 (m-80) REVERT: A 88 ARG cc_start: 0.7009 (ttm170) cc_final: 0.6728 (mtm-85) REVERT: A 103 TYR cc_start: 0.7966 (t80) cc_final: 0.7662 (t80) REVERT: A 190 ASP cc_start: 0.8192 (m-30) cc_final: 0.7890 (m-30) REVERT: A 365 LYS cc_start: 0.7865 (mptt) cc_final: 0.7535 (mppt) REVERT: A 747 MET cc_start: 0.7653 (ttp) cc_final: 0.7400 (ttp) REVERT: D 55 TYR cc_start: 0.8102 (m-80) cc_final: 0.7747 (m-80) REVERT: D 88 ARG cc_start: 0.6963 (ttm170) cc_final: 0.6683 (mtm-85) REVERT: D 190 ASP cc_start: 0.8177 (m-30) cc_final: 0.7878 (m-30) REVERT: D 210 ARG cc_start: 0.7108 (mtp85) cc_final: 0.6803 (mtp-110) REVERT: D 246 ARG cc_start: 0.7691 (mmp80) cc_final: 0.7489 (mmt-90) REVERT: D 365 LYS cc_start: 0.7869 (mptt) cc_final: 0.7533 (mppt) REVERT: B 55 TYR cc_start: 0.8105 (m-80) cc_final: 0.7751 (m-80) REVERT: B 88 ARG cc_start: 0.6999 (ttm170) cc_final: 0.6695 (mtm-85) REVERT: B 190 ASP cc_start: 0.8173 (m-30) cc_final: 0.7877 (m-30) REVERT: B 210 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6768 (mtp-110) REVERT: B 246 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7467 (mmt-90) REVERT: B 365 LYS cc_start: 0.7861 (mptt) cc_final: 0.7521 (mppt) REVERT: C 55 TYR cc_start: 0.8044 (m-80) cc_final: 0.7672 (m-80) REVERT: C 88 ARG cc_start: 0.7033 (ttm170) cc_final: 0.6720 (mtm-85) REVERT: C 190 ASP cc_start: 0.8197 (m-30) cc_final: 0.7889 (m-30) REVERT: C 365 LYS cc_start: 0.7857 (mptt) cc_final: 0.7513 (mppt) outliers start: 24 outliers final: 18 residues processed: 487 average time/residue: 2.4085 time to fit residues: 1409.1384 Evaluate side-chains 477 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 459 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 286 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23520 Z= 0.279 Angle : 0.643 6.546 31892 Z= 0.304 Chirality : 0.043 0.163 3580 Planarity : 0.003 0.053 4040 Dihedral : 10.642 131.383 3568 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.26 % Allowed : 16.23 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 2956 helix: 1.99 (0.13), residues: 1496 sheet: -0.02 (0.23), residues: 500 loop : -0.66 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 382 HIS 0.007 0.001 HIS A 390 PHE 0.016 0.002 PHE A 378 TYR 0.020 0.002 TYR B 43 ARG 0.009 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 469 time to evaluate : 3.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8095 (m-80) cc_final: 0.7742 (m-80) REVERT: A 88 ARG cc_start: 0.7032 (ttm170) cc_final: 0.6764 (mtm-85) REVERT: A 190 ASP cc_start: 0.8220 (m-30) cc_final: 0.7969 (m-30) REVERT: A 322 MET cc_start: 0.6851 (mmm) cc_final: 0.6642 (mmm) REVERT: A 365 LYS cc_start: 0.7830 (mptt) cc_final: 0.7530 (mppt) REVERT: D 55 TYR cc_start: 0.8106 (m-80) cc_final: 0.7681 (m-80) REVERT: D 88 ARG cc_start: 0.6989 (ttm170) cc_final: 0.6726 (mtm-85) REVERT: D 103 TYR cc_start: 0.7981 (t80) cc_final: 0.7678 (t80) REVERT: D 190 ASP cc_start: 0.8203 (m-30) cc_final: 0.7961 (m-30) REVERT: D 210 ARG cc_start: 0.7143 (mtp85) cc_final: 0.6884 (mtp-110) REVERT: D 365 LYS cc_start: 0.7839 (mptt) cc_final: 0.7515 (mppt) REVERT: B 55 TYR cc_start: 0.8110 (m-80) cc_final: 0.7687 (m-80) REVERT: B 88 ARG cc_start: 0.7063 (ttm170) cc_final: 0.6763 (mtm-85) REVERT: B 103 TYR cc_start: 0.7975 (t80) cc_final: 0.7672 (t80) REVERT: B 190 ASP cc_start: 0.8204 (m-30) cc_final: 0.7961 (m-30) REVERT: B 210 ARG cc_start: 0.7184 (mtp85) cc_final: 0.6861 (mtp-110) REVERT: B 365 LYS cc_start: 0.7842 (mptt) cc_final: 0.7528 (mppt) REVERT: C 55 TYR cc_start: 0.8082 (m-80) cc_final: 0.7639 (m-80) REVERT: C 88 ARG cc_start: 0.7087 (ttm170) cc_final: 0.6774 (mtm-85) REVERT: C 103 TYR cc_start: 0.7975 (t80) cc_final: 0.7678 (t80) REVERT: C 190 ASP cc_start: 0.8219 (m-30) cc_final: 0.7967 (m-30) REVERT: C 365 LYS cc_start: 0.7828 (mptt) cc_final: 0.7492 (mppt) REVERT: C 747 MET cc_start: 0.7698 (ttp) cc_final: 0.7390 (ttp) outliers start: 30 outliers final: 25 residues processed: 484 average time/residue: 2.3623 time to fit residues: 1361.7009 Evaluate side-chains 485 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 460 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23520 Z= 0.289 Angle : 0.646 6.381 31892 Z= 0.307 Chirality : 0.043 0.159 3580 Planarity : 0.003 0.059 4040 Dihedral : 10.469 130.165 3568 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.30 % Allowed : 16.99 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.16), residues: 2956 helix: 1.97 (0.13), residues: 1496 sheet: -0.04 (0.23), residues: 500 loop : -0.64 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 382 HIS 0.005 0.001 HIS B 390 PHE 0.009 0.001 PHE C 308 TYR 0.019 0.002 TYR D 43 ARG 0.011 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 470 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8111 (m-80) cc_final: 0.7699 (m-80) REVERT: A 88 ARG cc_start: 0.7060 (ttm170) cc_final: 0.6784 (mtm-85) REVERT: A 190 ASP cc_start: 0.8265 (m-30) cc_final: 0.8062 (m-30) REVERT: A 319 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6424 (tt0) REVERT: A 365 LYS cc_start: 0.7823 (mptt) cc_final: 0.7517 (mppt) REVERT: D 55 TYR cc_start: 0.8121 (m-80) cc_final: 0.7718 (m-80) REVERT: D 88 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6784 (mtm-85) REVERT: D 210 ARG cc_start: 0.7131 (mtp85) cc_final: 0.6872 (mtp-110) REVERT: D 319 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: D 365 LYS cc_start: 0.7814 (mptt) cc_final: 0.7512 (mppt) REVERT: B 55 TYR cc_start: 0.8124 (m-80) cc_final: 0.7715 (m-80) REVERT: B 88 ARG cc_start: 0.7075 (ttm170) cc_final: 0.6774 (mtm-85) REVERT: B 190 ASP cc_start: 0.8254 (m-30) cc_final: 0.8054 (m-30) REVERT: B 210 ARG cc_start: 0.7160 (mtp85) cc_final: 0.6918 (mtp-110) REVERT: B 365 LYS cc_start: 0.7816 (mptt) cc_final: 0.7506 (mppt) REVERT: C 55 TYR cc_start: 0.8100 (m-80) cc_final: 0.7685 (m-80) REVERT: C 190 ASP cc_start: 0.8263 (m-30) cc_final: 0.8060 (m-30) REVERT: C 319 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6409 (tt0) REVERT: C 365 LYS cc_start: 0.7819 (mptt) cc_final: 0.7499 (mppt) outliers start: 31 outliers final: 24 residues processed: 486 average time/residue: 2.2675 time to fit residues: 1313.8274 Evaluate side-chains 497 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 470 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 613 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23520 Z= 0.246 Angle : 0.627 6.253 31892 Z= 0.296 Chirality : 0.042 0.155 3580 Planarity : 0.003 0.070 4040 Dihedral : 10.188 130.655 3568 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.30 % Allowed : 17.37 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2956 helix: 2.10 (0.13), residues: 1492 sheet: -0.01 (0.23), residues: 500 loop : -0.62 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 382 HIS 0.006 0.001 HIS D 390 PHE 0.017 0.001 PHE C 378 TYR 0.017 0.001 TYR D 43 ARG 0.013 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 463 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8100 (m-80) cc_final: 0.7722 (m-80) REVERT: A 88 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6753 (mtm-85) REVERT: A 319 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: A 365 LYS cc_start: 0.7797 (mptt) cc_final: 0.7519 (mppt) REVERT: D 55 TYR cc_start: 0.8111 (m-80) cc_final: 0.7720 (m-80) REVERT: D 88 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6746 (mtm-85) REVERT: D 210 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6855 (mtp-110) REVERT: D 319 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: D 365 LYS cc_start: 0.7804 (mptt) cc_final: 0.7528 (mppt) REVERT: B 55 TYR cc_start: 0.8117 (m-80) cc_final: 0.7716 (m-80) REVERT: B 88 ARG cc_start: 0.7040 (ttm170) cc_final: 0.6753 (mtm-85) REVERT: B 210 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6912 (mtp-110) REVERT: B 365 LYS cc_start: 0.7806 (mptt) cc_final: 0.7527 (mppt) REVERT: C 55 TYR cc_start: 0.8091 (m-80) cc_final: 0.7685 (m-80) REVERT: C 319 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: C 365 LYS cc_start: 0.7798 (mptt) cc_final: 0.7505 (mppt) outliers start: 31 outliers final: 19 residues processed: 480 average time/residue: 2.1410 time to fit residues: 1223.4114 Evaluate side-chains 475 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 453 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 251 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 HIS ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN B 126 ASN ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23520 Z= 0.230 Angle : 0.623 6.275 31892 Z= 0.294 Chirality : 0.042 0.155 3580 Planarity : 0.003 0.070 4040 Dihedral : 9.954 130.505 3568 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.01 % Allowed : 17.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 2956 helix: 2.14 (0.13), residues: 1492 sheet: -0.05 (0.23), residues: 476 loop : -0.57 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 382 HIS 0.005 0.001 HIS D 390 PHE 0.008 0.001 PHE C 308 TYR 0.020 0.001 TYR B 43 ARG 0.015 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 449 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8098 (m-80) cc_final: 0.7709 (m-80) REVERT: A 319 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: A 365 LYS cc_start: 0.7787 (mptt) cc_final: 0.7513 (mppt) REVERT: A 374 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.6764 (mtm-85) REVERT: D 55 TYR cc_start: 0.8100 (m-80) cc_final: 0.7711 (m-80) REVERT: D 88 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6742 (mtm-85) REVERT: D 210 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6818 (mtp-110) REVERT: D 319 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6437 (tt0) REVERT: D 365 LYS cc_start: 0.7820 (mptt) cc_final: 0.7544 (mppt) REVERT: B 55 TYR cc_start: 0.8101 (m-80) cc_final: 0.7708 (m-80) REVERT: B 210 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6892 (mtp-110) REVERT: B 365 LYS cc_start: 0.7819 (mptt) cc_final: 0.7542 (mppt) REVERT: C 55 TYR cc_start: 0.8082 (m-80) cc_final: 0.7678 (m-80) REVERT: C 319 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6424 (tt0) REVERT: C 365 LYS cc_start: 0.7787 (mptt) cc_final: 0.7499 (mppt) outliers start: 24 outliers final: 18 residues processed: 466 average time/residue: 2.0444 time to fit residues: 1138.9186 Evaluate side-chains 470 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 449 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23520 Z= 0.210 Angle : 0.613 6.272 31892 Z= 0.287 Chirality : 0.041 0.150 3580 Planarity : 0.003 0.071 4040 Dihedral : 9.670 129.176 3568 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.88 % Allowed : 17.79 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.16), residues: 2956 helix: 2.22 (0.13), residues: 1492 sheet: -0.02 (0.23), residues: 476 loop : -0.52 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 382 HIS 0.004 0.001 HIS B 390 PHE 0.016 0.001 PHE A 378 TYR 0.018 0.001 TYR B 43 ARG 0.015 0.000 ARG C 210 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5912 Ramachandran restraints generated. 2956 Oldfield, 0 Emsley, 2956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 458 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8081 (m-80) cc_final: 0.7685 (m-80) REVERT: A 365 LYS cc_start: 0.7801 (mptt) cc_final: 0.7524 (mppt) REVERT: A 374 ARG cc_start: 0.7494 (mtt-85) cc_final: 0.6766 (mtm-85) REVERT: D 55 TYR cc_start: 0.8093 (m-80) cc_final: 0.7707 (m-80) REVERT: D 88 ARG cc_start: 0.6977 (ttm170) cc_final: 0.6720 (mtm-85) REVERT: D 210 ARG cc_start: 0.7059 (mtp85) cc_final: 0.6800 (mtp-110) REVERT: D 319 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6431 (tt0) REVERT: D 365 LYS cc_start: 0.7820 (mptt) cc_final: 0.7542 (mppt) REVERT: D 374 ARG cc_start: 0.7501 (mtt-85) cc_final: 0.6766 (mtm-85) REVERT: B 55 TYR cc_start: 0.8097 (m-80) cc_final: 0.7716 (m-80) REVERT: B 210 ARG cc_start: 0.7110 (mtp85) cc_final: 0.6878 (mtp-110) REVERT: B 365 LYS cc_start: 0.7805 (mptt) cc_final: 0.7538 (mppt) REVERT: B 374 ARG cc_start: 0.7506 (mtt-85) cc_final: 0.6764 (mtm-85) REVERT: C 55 TYR cc_start: 0.8071 (m-80) cc_final: 0.7679 (m-80) REVERT: C 365 LYS cc_start: 0.7814 (mptt) cc_final: 0.7522 (mppt) outliers start: 21 outliers final: 18 residues processed: 474 average time/residue: 1.8740 time to fit residues: 1056.9720 Evaluate side-chains 473 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 454 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 705 ASP Chi-restraints excluded: chain D residue 728 ASP Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 705 ASP Chi-restraints excluded: chain C residue 728 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 216 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.154669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124056 restraints weight = 76276.775| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.79 r_work: 0.3110 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23520 Z= 0.173 Angle : 0.598 6.567 31892 Z= 0.279 Chirality : 0.041 0.145 3580 Planarity : 0.003 0.076 4040 Dihedral : 9.305 127.262 3568 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.55 % Allowed : 18.33 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2956 helix: 2.36 (0.13), residues: 1492 sheet: 0.03 (0.23), residues: 472 loop : -0.42 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 382 HIS 0.004 0.001 HIS B 390 PHE 0.017 0.001 PHE B 700 TYR 0.017 0.001 TYR B 43 ARG 0.018 0.000 ARG C 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18481.78 seconds wall clock time: 322 minutes 45.88 seconds (19365.88 seconds total)