Starting phenix.real_space_refine on Wed Aug 27 02:11:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_43747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_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 { model { file = "/net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_43747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_43747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_43747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w2g_43747/08_2025/8w2g_43747.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.335 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 8.07, per 1000 atoms: 0.18 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: 4.31 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.64 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: 13.54 Time building geometry restraints manager: 5.90 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.340 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 45.870 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 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:6.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.180 ------------------------------------------------------------------------------- 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= 0.691 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG D 485 TYR 0.014 0.002 TYR C 674 PHE 0.012 0.002 PHE A 439 TRP 0.012 0.002 TRP A 741 HIS 0.006 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.01407 (23520) covalent geometry : angle 0.87290 (31892) hydrogen bonds : bond 0.16962 ( 1177) hydrogen bonds : angle 6.25014 ( 3408) *********************** 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 : 1.236 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: 0.7708 (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: 0.7602 (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: 0.7595 (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: 0.7539 (m-30) REVERT: B 379 GLU cc_start: 0.7301 (tp30) cc_final: 0.6896 (tm-30) REVERT: B 383 ASN cc_start: 0.7343 (m-40) cc_final: 0.7091 (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: 0.7581 (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: 1.2550 time to fit residues: 995.0829 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 : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 353 GLN C 75 ASN C 353 GLN C 448 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122894 restraints weight = 76379.670| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.75 r_work: 0.3164 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2032 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= 0.136 Angle : 0.651 7.221 31892 Z= 0.311 Chirality : 0.042 0.158 3580 Planarity : 0.004 0.044 4040 Dihedral : 13.203 151.064 3568 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.01 % Allowed : 12.58 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.15), residues: 2956 helix: 1.60 (0.13), residues: 1468 sheet: -0.14 (0.22), residues: 476 loop : -0.69 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 210 TYR 0.013 0.001 TYR C 674 PHE 0.013 0.001 PHE C 378 TRP 0.014 0.001 TRP D 382 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00290 (23520) covalent geometry : angle 0.65104 (31892) hydrogen bonds : bond 0.04744 ( 1177) hydrogen bonds : angle 4.52869 ( 3408) *********************** 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 535 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 511 time to evaluate : 1.254 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: 0.8131 (m-80) cc_final: 0.7676 (m-80) REVERT: A 88 ARG cc_start: 0.7265 (ttm110) cc_final: 0.6937 (mtm-85) REVERT: A 90 LYS cc_start: 0.7069 (tppp) cc_final: 0.6789 (tmmt) REVERT: A 190 ASP cc_start: 0.8057 (m-30) cc_final: 0.7804 (m-30) REVERT: A 210 ARG cc_start: 0.7238 (ttt-90) cc_final: 0.6923 (mtp-110) REVERT: A 694 TYR cc_start: 0.7808 (t80) cc_final: 0.7569 (t80) REVERT: D 55 TYR cc_start: 0.8132 (m-80) cc_final: 0.7691 (m-80) REVERT: D 88 ARG cc_start: 0.7269 (ttm110) cc_final: 0.6964 (mtm-85) REVERT: D 90 LYS cc_start: 0.7070 (tppp) cc_final: 0.6807 (tmmt) REVERT: D 190 ASP cc_start: 0.8040 (m-30) cc_final: 0.7648 (m-30) REVERT: B 55 TYR cc_start: 0.8126 (m-80) cc_final: 0.7690 (m-80) REVERT: B 88 ARG cc_start: 0.7259 (ttm110) cc_final: 0.6949 (mtm-85) REVERT: B 90 LYS cc_start: 0.7057 (tppp) cc_final: 0.6803 (tmmt) REVERT: B 190 ASP cc_start: 0.8048 (m-30) cc_final: 0.7794 (m-30) REVERT: B 694 TYR cc_start: 0.7811 (t80) cc_final: 0.7575 (t80) REVERT: C 55 TYR cc_start: 0.8015 (m-80) cc_final: 0.7588 (m-80) REVERT: C 88 ARG cc_start: 0.7266 (ttm110) cc_final: 0.6926 (mtm-85) REVERT: C 90 LYS cc_start: 0.7057 (tppp) cc_final: 0.6792 (tmmt) REVERT: C 190 ASP cc_start: 0.8064 (m-30) cc_final: 0.7815 (m-30) REVERT: C 210 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.6978 (mtp-110) REVERT: C 694 TYR cc_start: 0.7835 (t80) cc_final: 0.7584 (t80) outliers start: 24 outliers final: 6 residues processed: 529 average time/residue: 1.2359 time to fit residues: 773.3887 Evaluate side-chains 480 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 474 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN C 75 ASN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.148298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.117206 restraints weight = 77129.266| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.75 r_work: 0.3140 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2408 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= 0.196 Angle : 0.660 7.088 31892 Z= 0.314 Chirality : 0.043 0.161 3580 Planarity : 0.003 0.035 4040 Dihedral : 12.310 144.261 3568 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.22 % Allowed : 14.01 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.15), residues: 2956 helix: 1.82 (0.13), residues: 1488 sheet: -0.07 (0.22), residues: 496 loop : -0.74 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 672 TYR 0.016 0.002 TYR C 103 PHE 0.010 0.002 PHE C 308 TRP 0.013 0.001 TRP B 382 HIS 0.003 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00440 (23520) covalent geometry : angle 0.65985 (31892) hydrogen bonds : bond 0.04568 ( 1177) hydrogen bonds : angle 4.41510 ( 3408) *********************** 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 504 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 475 time to evaluate : 1.253 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: 0.8180 (m-80) cc_final: 0.7647 (m-80) REVERT: A 88 ARG cc_start: 0.7324 (ttm170) cc_final: 0.7017 (mtm-85) REVERT: A 90 LYS cc_start: 0.7121 (tppp) cc_final: 0.6795 (tmmt) REVERT: A 190 ASP cc_start: 0.8372 (m-30) cc_final: 0.8021 (m-30) REVERT: A 210 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.6968 (mtp-110) REVERT: A 694 TYR cc_start: 0.7846 (t80) cc_final: 0.7640 (t80) REVERT: D 55 TYR cc_start: 0.8183 (m-80) cc_final: 0.7646 (m-80) REVERT: D 88 ARG cc_start: 0.7326 (ttm170) cc_final: 0.7030 (mtm-85) REVERT: D 90 LYS cc_start: 0.7137 (tppp) cc_final: 0.6825 (tmmt) REVERT: D 190 ASP cc_start: 0.8267 (m-30) cc_final: 0.8036 (m-30) REVERT: D 210 ARG cc_start: 0.7226 (mtp85) cc_final: 0.6884 (mtp-110) REVERT: B 55 TYR cc_start: 0.8190 (m-80) cc_final: 0.7658 (m-80) REVERT: B 88 ARG cc_start: 0.7330 (ttm110) cc_final: 0.7016 (mtm-85) REVERT: B 90 LYS cc_start: 0.7124 (tppp) cc_final: 0.6821 (tmmt) REVERT: B 190 ASP cc_start: 0.8363 (m-30) cc_final: 0.7998 (m-30) REVERT: B 210 ARG cc_start: 0.7271 (mtp85) cc_final: 0.6801 (mtp-110) REVERT: B 694 TYR cc_start: 0.7836 (t80) cc_final: 0.7628 (t80) REVERT: C 55 TYR cc_start: 0.8082 (m-80) cc_final: 0.7555 (m-80) REVERT: C 88 ARG cc_start: 0.7333 (ttm170) cc_final: 0.6996 (mtm-85) REVERT: C 90 LYS cc_start: 0.7117 (tppp) cc_final: 0.6797 (tmmt) REVERT: C 190 ASP cc_start: 0.8375 (m-30) cc_final: 0.8023 (m-30) REVERT: C 210 ARG cc_start: 0.7209 (ttt-90) cc_final: 0.6914 (mtp-110) REVERT: C 694 TYR cc_start: 0.7851 (t80) cc_final: 0.7643 (t80) outliers start: 29 outliers final: 24 residues processed: 487 average time/residue: 1.1342 time to fit residues: 654.1739 Evaluate side-chains 477 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 453 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 291 THR Chi-restraints excluded: chain C residue 448 GLN 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 220 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 174 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.153824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123102 restraints weight = 76238.815| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.74 r_work: 0.3158 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23520 Z= 0.145 Angle : 0.622 7.073 31892 Z= 0.292 Chirality : 0.041 0.153 3580 Planarity : 0.003 0.024 4040 Dihedral : 11.090 138.837 3568 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.09 % Allowed : 15.18 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.16), residues: 2956 helix: 2.04 (0.14), residues: 1492 sheet: 0.04 (0.22), residues: 496 loop : -0.61 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.014 0.001 TYR A 103 PHE 0.013 0.001 PHE D 378 TRP 0.012 0.001 TRP D 382 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00322 (23520) covalent geometry : angle 0.62200 (31892) hydrogen bonds : bond 0.03933 ( 1177) hydrogen bonds : angle 4.20906 ( 3408) *********************** 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 491 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 465 time to evaluate : 0.984 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: A 55 TYR cc_start: 0.8181 (m-80) cc_final: 0.7665 (m-80) REVERT: A 88 ARG cc_start: 0.7252 (ttm170) cc_final: 0.6852 (mtm-85) REVERT: A 90 LYS cc_start: 0.7169 (tppp) cc_final: 0.6854 (tmmt) REVERT: A 103 TYR cc_start: 0.7941 (t80) cc_final: 0.7669 (t80) REVERT: A 190 ASP cc_start: 0.8505 (m-30) cc_final: 0.8171 (m-30) REVERT: A 210 ARG cc_start: 0.7238 (ttt-90) cc_final: 0.6961 (mtp-110) REVERT: A 269 ARG cc_start: 0.6153 (mmm160) cc_final: 0.5611 (mmt180) REVERT: A 322 MET cc_start: 0.6825 (mmm) cc_final: 0.6539 (mmm) REVERT: A 365 LYS cc_start: 0.7626 (mptt) cc_final: 0.7152 (mppt) REVERT: D 55 TYR cc_start: 0.8202 (m-80) cc_final: 0.7681 (m-80) REVERT: D 88 ARG cc_start: 0.7246 (ttm170) cc_final: 0.6869 (mtm-85) REVERT: D 90 LYS cc_start: 0.7183 (tppp) cc_final: 0.6887 (tmmt) REVERT: D 103 TYR cc_start: 0.7928 (t80) cc_final: 0.7658 (t80) REVERT: D 190 ASP cc_start: 0.8455 (m-30) cc_final: 0.8131 (m-30) REVERT: D 210 ARG cc_start: 0.7241 (mtp85) cc_final: 0.6852 (mtp-110) REVERT: D 269 ARG cc_start: 0.5956 (mmm160) cc_final: 0.5719 (mmt-90) REVERT: D 349 MET cc_start: 0.7637 (mmm) cc_final: 0.7363 (mmm) REVERT: D 365 LYS cc_start: 0.7645 (mptt) cc_final: 0.7184 (mppt) REVERT: B 55 TYR cc_start: 0.8195 (m-80) cc_final: 0.7681 (m-80) REVERT: B 88 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6868 (mtm-85) REVERT: B 90 LYS cc_start: 0.7172 (tppp) cc_final: 0.6884 (tmmt) REVERT: B 103 TYR cc_start: 0.7922 (t80) cc_final: 0.7662 (t80) REVERT: B 190 ASP cc_start: 0.8473 (m-30) cc_final: 0.8137 (m-30) REVERT: B 210 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6804 (mtp-110) REVERT: B 269 ARG cc_start: 0.5977 (mmm160) cc_final: 0.5734 (mmt-90) REVERT: B 365 LYS cc_start: 0.7648 (mptt) cc_final: 0.7184 (mppt) REVERT: C 55 TYR cc_start: 0.8100 (m-80) cc_final: 0.7547 (m-80) REVERT: C 88 ARG cc_start: 0.7281 (ttm170) cc_final: 0.6855 (mtm-85) REVERT: C 90 LYS cc_start: 0.7161 (tppp) cc_final: 0.6859 (tmmt) REVERT: C 103 TYR cc_start: 0.7919 (t80) cc_final: 0.7656 (t80) REVERT: C 190 ASP cc_start: 0.8501 (m-30) cc_final: 0.8164 (m-30) REVERT: C 210 ARG cc_start: 0.7187 (ttt-90) cc_final: 0.6899 (mtp-110) REVERT: C 322 MET cc_start: 0.6845 (mmm) cc_final: 0.6565 (mmm) REVERT: C 365 LYS cc_start: 0.7623 (mptt) cc_final: 0.7152 (mppt) outliers start: 26 outliers final: 23 residues processed: 477 average time/residue: 1.0068 time to fit residues: 567.4494 Evaluate side-chains 473 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 450 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 GLN 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 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 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 291 THR Chi-restraints excluded: chain C residue 448 GLN 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 26 optimal weight: 0.3980 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 213 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 180 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.154843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.124139 restraints weight = 75545.980| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.72 r_work: 0.3158 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2754 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= 0.124 Angle : 0.600 7.126 31892 Z= 0.280 Chirality : 0.041 0.149 3580 Planarity : 0.003 0.030 4040 Dihedral : 10.361 134.970 3568 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.92 % Allowed : 15.60 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.16), residues: 2956 helix: 2.22 (0.14), residues: 1492 sheet: 0.10 (0.22), residues: 496 loop : -0.51 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 485 TYR 0.015 0.001 TYR B 43 PHE 0.008 0.001 PHE C 308 TRP 0.011 0.001 TRP C 382 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00274 (23520) covalent geometry : angle 0.59956 (31892) hydrogen bonds : bond 0.03641 ( 1177) hydrogen bonds : angle 4.10483 ( 3408) *********************** 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 495 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 473 time to evaluate : 1.223 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 TYR cc_start: 0.8177 (m-80) cc_final: 0.7656 (m-80) REVERT: A 88 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6933 (mtm-85) REVERT: A 90 LYS cc_start: 0.7164 (tppp) cc_final: 0.6861 (tmmt) REVERT: A 103 TYR cc_start: 0.7915 (t80) cc_final: 0.7652 (t80) REVERT: A 190 ASP cc_start: 0.8501 (m-30) cc_final: 0.8151 (m-30) REVERT: A 322 MET cc_start: 0.6764 (mmm) cc_final: 0.6528 (mmm) REVERT: A 365 LYS cc_start: 0.7576 (mptt) cc_final: 0.7108 (mppt) REVERT: D 55 TYR cc_start: 0.8193 (m-80) cc_final: 0.7675 (m-80) REVERT: D 88 ARG cc_start: 0.7239 (ttm170) cc_final: 0.6942 (mtm-85) REVERT: D 90 LYS cc_start: 0.7168 (tppp) cc_final: 0.6867 (tmmt) REVERT: D 103 TYR cc_start: 0.7901 (t80) cc_final: 0.7641 (t80) REVERT: D 190 ASP cc_start: 0.8472 (m-30) cc_final: 0.8145 (m-30) REVERT: D 210 ARG cc_start: 0.7231 (mtp85) cc_final: 0.6878 (mtp-110) REVERT: D 269 ARG cc_start: 0.5908 (mmm160) cc_final: 0.5481 (mmt180) REVERT: D 349 MET cc_start: 0.7711 (mmm) cc_final: 0.7505 (mmm) REVERT: D 365 LYS cc_start: 0.7611 (mptt) cc_final: 0.7144 (mppt) REVERT: B 55 TYR cc_start: 0.8181 (m-80) cc_final: 0.7665 (m-80) REVERT: B 88 ARG cc_start: 0.7286 (ttm170) cc_final: 0.6937 (mtm-85) REVERT: B 90 LYS cc_start: 0.7144 (tppp) cc_final: 0.6872 (tmmt) REVERT: B 103 TYR cc_start: 0.7887 (t80) cc_final: 0.7626 (t80) REVERT: B 190 ASP cc_start: 0.8461 (m-30) cc_final: 0.8128 (m-30) REVERT: B 210 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6887 (mtp-110) REVERT: B 269 ARG cc_start: 0.5962 (mmm160) cc_final: 0.5545 (mmt180) REVERT: B 365 LYS cc_start: 0.7612 (mptt) cc_final: 0.7140 (mppt) REVERT: C 55 TYR cc_start: 0.8088 (m-80) cc_final: 0.7533 (m-80) REVERT: C 88 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6936 (mtm-85) REVERT: C 90 LYS cc_start: 0.7151 (tppp) cc_final: 0.6859 (tmmt) REVERT: C 103 TYR cc_start: 0.7882 (t80) cc_final: 0.7620 (t80) REVERT: C 190 ASP cc_start: 0.8483 (m-30) cc_final: 0.8147 (m-30) REVERT: C 322 MET cc_start: 0.6785 (mmm) cc_final: 0.6551 (mmm) REVERT: C 349 MET cc_start: 0.7717 (mmm) cc_final: 0.7477 (mmt) REVERT: C 365 LYS cc_start: 0.7577 (mptt) cc_final: 0.7089 (mppt) outliers start: 22 outliers final: 17 residues processed: 483 average time/residue: 1.0237 time to fit residues: 585.9184 Evaluate side-chains 477 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 460 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 632 ASP Chi-restraints excluded: chain B residue 705 ASP Chi-restraints excluded: chain B residue 728 ASP Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 618 ASP 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 194 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.116352 restraints weight = 76911.191| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.75 r_work: 0.3103 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23520 Z= 0.229 Angle : 0.669 6.706 31892 Z= 0.319 Chirality : 0.044 0.168 3580 Planarity : 0.003 0.032 4040 Dihedral : 10.483 131.679 3568 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.47 % Allowed : 15.65 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.15), residues: 2956 helix: 1.95 (0.13), residues: 1496 sheet: 0.02 (0.23), residues: 500 loop : -0.64 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 485 TYR 0.017 0.002 TYR B 43 PHE 0.016 0.002 PHE C 378 TRP 0.011 0.001 TRP B 382 HIS 0.002 0.001 HIS C 436 Details of bonding type rmsd covalent geometry : bond 0.00525 (23520) covalent geometry : angle 0.66884 (31892) hydrogen bonds : bond 0.04385 ( 1177) hydrogen bonds : angle 4.33286 ( 3408) *********************** 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 515 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 480 time to evaluate : 1.257 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: 0.8176 (m-80) cc_final: 0.7784 (m-80) REVERT: A 88 ARG cc_start: 0.7355 (ttm170) cc_final: 0.7037 (mtm-85) REVERT: A 90 LYS cc_start: 0.7175 (tppp) cc_final: 0.6876 (tmmt) REVERT: A 190 ASP cc_start: 0.8534 (m-30) cc_final: 0.8260 (m-30) REVERT: A 210 ARG cc_start: 0.7305 (ttt-90) cc_final: 0.7105 (mtp-110) REVERT: A 322 MET cc_start: 0.6882 (mmm) cc_final: 0.6643 (mmm) REVERT: A 365 LYS cc_start: 0.7553 (mptt) cc_final: 0.7116 (mppt) REVERT: A 747 MET cc_start: 0.7912 (ttp) cc_final: 0.7620 (ttp) REVERT: D 55 TYR cc_start: 0.8203 (m-80) cc_final: 0.7581 (m-80) REVERT: D 88 ARG cc_start: 0.7337 (ttm170) cc_final: 0.7025 (mtm-85) REVERT: D 90 LYS cc_start: 0.7236 (tppp) cc_final: 0.6930 (tmmt) REVERT: D 190 ASP cc_start: 0.8482 (m-30) cc_final: 0.8218 (m-30) REVERT: D 210 ARG cc_start: 0.7339 (mtp85) cc_final: 0.7012 (mtp-110) REVERT: D 269 ARG cc_start: 0.5989 (mmm160) cc_final: 0.5492 (mmt180) REVERT: D 365 LYS cc_start: 0.7587 (mptt) cc_final: 0.7152 (mppt) REVERT: B 55 TYR cc_start: 0.8212 (m-80) cc_final: 0.7606 (m-80) REVERT: B 88 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7002 (mtm-85) REVERT: B 90 LYS cc_start: 0.7167 (tppp) cc_final: 0.6919 (tmmt) REVERT: B 190 ASP cc_start: 0.8515 (m-30) cc_final: 0.8243 (m-30) REVERT: B 210 ARG cc_start: 0.7295 (mtp85) cc_final: 0.6860 (mtp-110) REVERT: B 269 ARG cc_start: 0.6017 (mmm160) cc_final: 0.5514 (mmt180) REVERT: B 365 LYS cc_start: 0.7577 (mptt) cc_final: 0.7142 (mppt) REVERT: C 55 TYR cc_start: 0.8157 (m-80) cc_final: 0.7770 (m-80) REVERT: C 88 ARG cc_start: 0.7360 (ttm170) cc_final: 0.7019 (mtm-85) REVERT: C 90 LYS cc_start: 0.7171 (tppp) cc_final: 0.6887 (tmmt) REVERT: C 190 ASP cc_start: 0.8532 (m-30) cc_final: 0.8253 (m-30) REVERT: C 322 MET cc_start: 0.6874 (mmm) cc_final: 0.6629 (mmm) REVERT: C 365 LYS cc_start: 0.7547 (mptt) cc_final: 0.7102 (mppt) REVERT: C 747 MET cc_start: 0.7904 (ttp) cc_final: 0.7612 (ttp) outliers start: 35 outliers final: 29 residues processed: 496 average time/residue: 0.8476 time to fit residues: 498.0249 Evaluate side-chains 498 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 469 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 613 GLU 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 131 GLU Chi-restraints excluded: chain D residue 291 THR 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 119 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 391 GLN 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 486 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 618 ASP 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 138 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 151 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 126 ASN B 391 GLN C 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.151804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.121040 restraints weight = 76126.612| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.72 r_work: 0.3120 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23520 Z= 0.172 Angle : 0.634 6.454 31892 Z= 0.300 Chirality : 0.042 0.156 3580 Planarity : 0.003 0.039 4040 Dihedral : 10.289 130.856 3568 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.01 % Allowed : 17.11 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.16), residues: 2956 helix: 2.06 (0.13), residues: 1496 sheet: -0.05 (0.23), residues: 500 loop : -0.54 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.014 0.001 TYR B 43 PHE 0.009 0.001 PHE A 308 TRP 0.011 0.001 TRP D 382 HIS 0.003 0.001 HIS B 453 Details of bonding type rmsd covalent geometry : bond 0.00388 (23520) covalent geometry : angle 0.63359 (31892) hydrogen bonds : bond 0.04036 ( 1177) hydrogen bonds : angle 4.22744 ( 3408) *********************** 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 500 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 476 time to evaluate : 0.679 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: A 55 TYR cc_start: 0.8172 (m-80) cc_final: 0.7598 (m-80) REVERT: A 88 ARG cc_start: 0.7336 (ttm170) cc_final: 0.7012 (mtm-85) REVERT: A 90 LYS cc_start: 0.7200 (tppp) cc_final: 0.6853 (tmmt) REVERT: A 103 TYR cc_start: 0.7957 (t80) cc_final: 0.7654 (t80) REVERT: A 190 ASP cc_start: 0.8531 (m-30) cc_final: 0.8269 (m-30) REVERT: A 210 ARG cc_start: 0.7290 (ttt-90) cc_final: 0.7072 (mtp-110) REVERT: A 269 ARG cc_start: 0.5919 (mmm160) cc_final: 0.5589 (mmt-90) REVERT: A 322 MET cc_start: 0.6815 (mmm) cc_final: 0.6557 (mmm) REVERT: A 365 LYS cc_start: 0.7581 (mptt) cc_final: 0.7152 (mppt) REVERT: A 513 ARG cc_start: 0.7571 (mtp-110) cc_final: 0.7007 (mtm180) REVERT: D 55 TYR cc_start: 0.8202 (m-80) cc_final: 0.7638 (m-80) REVERT: D 88 ARG cc_start: 0.7340 (ttm170) cc_final: 0.7027 (mtm-85) REVERT: D 90 LYS cc_start: 0.7212 (tppp) cc_final: 0.6915 (tmmt) REVERT: D 103 TYR cc_start: 0.7950 (t80) cc_final: 0.7648 (t80) REVERT: D 190 ASP cc_start: 0.8524 (m-30) cc_final: 0.8264 (m-30) REVERT: D 210 ARG cc_start: 0.7329 (mtp85) cc_final: 0.7006 (mtp-110) REVERT: D 319 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: D 365 LYS cc_start: 0.7581 (mptt) cc_final: 0.7154 (mppt) REVERT: D 513 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7070 (mtm180) REVERT: B 55 TYR cc_start: 0.8203 (m-80) cc_final: 0.7641 (m-80) REVERT: B 88 ARG cc_start: 0.7345 (ttm170) cc_final: 0.7005 (mtm-85) REVERT: B 90 LYS cc_start: 0.7156 (tppp) cc_final: 0.6906 (tmmt) REVERT: B 103 TYR cc_start: 0.7922 (t80) cc_final: 0.7631 (t80) REVERT: B 190 ASP cc_start: 0.8525 (m-30) cc_final: 0.8269 (m-30) REVERT: B 210 ARG cc_start: 0.7308 (mtp85) cc_final: 0.6979 (mtp-110) REVERT: B 365 LYS cc_start: 0.7584 (mptt) cc_final: 0.7156 (mppt) REVERT: B 513 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.7077 (mtm180) REVERT: C 55 TYR cc_start: 0.8175 (m-80) cc_final: 0.7567 (m-80) REVERT: C 88 ARG cc_start: 0.7369 (ttm170) cc_final: 0.7023 (mtm-85) REVERT: C 90 LYS cc_start: 0.7150 (tppp) cc_final: 0.6883 (tmmt) REVERT: C 103 TYR cc_start: 0.7927 (t80) cc_final: 0.7635 (t80) REVERT: C 190 ASP cc_start: 0.8526 (m-30) cc_final: 0.8255 (m-30) REVERT: C 322 MET cc_start: 0.6817 (mmm) cc_final: 0.6561 (mmm) REVERT: C 365 LYS cc_start: 0.7562 (mptt) cc_final: 0.7111 (mppt) REVERT: C 513 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7013 (mtm180) outliers start: 24 outliers final: 20 residues processed: 491 average time/residue: 0.7056 time to fit residues: 413.4342 Evaluate side-chains 492 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 471 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 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 119 ASP Chi-restraints excluded: chain B residue 291 THR 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 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 8 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 144 optimal weight: 0.4980 chunk 136 optimal weight: 0.4980 chunk 250 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.155789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.124509 restraints weight = 76237.043| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.83 r_work: 0.3096 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23520 Z= 0.127 Angle : 0.599 6.282 31892 Z= 0.280 Chirality : 0.041 0.147 3580 Planarity : 0.003 0.045 4040 Dihedral : 9.800 130.486 3568 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.09 % Allowed : 17.16 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.16), residues: 2956 helix: 2.29 (0.14), residues: 1492 sheet: 0.01 (0.22), residues: 496 loop : -0.43 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 210 TYR 0.018 0.001 TYR D 43 PHE 0.015 0.001 PHE A 378 TRP 0.012 0.001 TRP B 382 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00282 (23520) covalent geometry : angle 0.59919 (31892) hydrogen bonds : bond 0.03596 ( 1177) hydrogen bonds : angle 4.07372 ( 3408) *********************** 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 501 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 475 time to evaluate : 0.706 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: A 55 TYR cc_start: 0.8168 (m-80) cc_final: 0.7584 (m-80) REVERT: A 88 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6965 (mtm-85) REVERT: A 90 LYS cc_start: 0.7176 (tppp) cc_final: 0.6837 (tmmt) REVERT: A 103 TYR cc_start: 0.7897 (t80) cc_final: 0.7608 (t80) REVERT: A 190 ASP cc_start: 0.8587 (m-30) cc_final: 0.8328 (m-30) REVERT: A 210 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6983 (mtp-110) REVERT: A 269 ARG cc_start: 0.5831 (mmm160) cc_final: 0.5517 (mmt-90) REVERT: A 322 MET cc_start: 0.6802 (mmm) cc_final: 0.6517 (mmm) REVERT: A 365 LYS cc_start: 0.7527 (mptt) cc_final: 0.7097 (mppt) REVERT: A 513 ARG cc_start: 0.7601 (mtp-110) cc_final: 0.7117 (mtm180) REVERT: D 55 TYR cc_start: 0.8187 (m-80) cc_final: 0.7601 (m-80) REVERT: D 88 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6947 (mtm-85) REVERT: D 90 LYS cc_start: 0.7184 (tppp) cc_final: 0.6897 (tmmt) REVERT: D 103 TYR cc_start: 0.7856 (t80) cc_final: 0.7576 (t80) REVERT: D 190 ASP cc_start: 0.8572 (m-30) cc_final: 0.8311 (m-30) REVERT: D 210 ARG cc_start: 0.7175 (mtp85) cc_final: 0.6835 (mtp-110) REVERT: D 269 ARG cc_start: 0.6049 (mmm160) cc_final: 0.5462 (mmt180) REVERT: D 319 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: D 365 LYS cc_start: 0.7529 (mptt) cc_final: 0.7100 (mppt) REVERT: D 513 ARG cc_start: 0.7626 (mtp-110) cc_final: 0.7128 (mtm180) REVERT: B 55 TYR cc_start: 0.8175 (m-80) cc_final: 0.7615 (m-80) REVERT: B 88 ARG cc_start: 0.7340 (ttm170) cc_final: 0.6995 (mtm-85) REVERT: B 90 LYS cc_start: 0.7187 (tppp) cc_final: 0.6893 (tmmt) REVERT: B 103 TYR cc_start: 0.7862 (t80) cc_final: 0.7582 (t80) REVERT: B 190 ASP cc_start: 0.8589 (m-30) cc_final: 0.8330 (m-30) REVERT: B 210 ARG cc_start: 0.7216 (mtp85) cc_final: 0.6897 (mtp-110) REVERT: B 246 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7125 (mmt-90) REVERT: B 269 ARG cc_start: 0.6052 (mmm160) cc_final: 0.5465 (mmt180) REVERT: B 365 LYS cc_start: 0.7548 (mptt) cc_final: 0.7109 (mppt) REVERT: B 391 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7535 (tt0) REVERT: B 513 ARG cc_start: 0.7642 (mtp-110) cc_final: 0.7125 (mtm180) REVERT: B 648 LYS cc_start: 0.8141 (tptt) cc_final: 0.7867 (tptp) REVERT: C 55 TYR cc_start: 0.8128 (m-80) cc_final: 0.7776 (m-80) REVERT: C 88 ARG cc_start: 0.7344 (ttm170) cc_final: 0.6991 (mtm-85) REVERT: C 90 LYS cc_start: 0.7158 (tppp) cc_final: 0.6865 (tmmt) REVERT: C 103 TYR cc_start: 0.7865 (t80) cc_final: 0.7584 (t80) REVERT: C 190 ASP cc_start: 0.8565 (m-30) cc_final: 0.8295 (m-30) REVERT: C 246 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6898 (mmt90) REVERT: C 322 MET cc_start: 0.6794 (mmm) cc_final: 0.6509 (mmm) REVERT: C 365 LYS cc_start: 0.7521 (mptt) cc_final: 0.7070 (mppt) REVERT: C 513 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7109 (mtm180) outliers start: 26 outliers final: 15 residues processed: 488 average time/residue: 0.7096 time to fit residues: 414.9813 Evaluate side-chains 484 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 465 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 ASP Chi-restraints excluded: chain A residue 728 ASP Chi-restraints excluded: chain D residue 319 GLU 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 246 ARG Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 391 GLN 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 246 ARG Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 613 GLU 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 51 optimal weight: 0.6980 chunk 29 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 218 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.156269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.124913 restraints weight = 75850.384| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.84 r_work: 0.3105 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23520 Z= 0.120 Angle : 0.592 6.213 31892 Z= 0.275 Chirality : 0.041 0.154 3580 Planarity : 0.003 0.039 4040 Dihedral : 9.433 130.943 3568 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.80 % Allowed : 17.58 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.16), residues: 2956 helix: 2.41 (0.14), residues: 1492 sheet: -0.02 (0.23), residues: 472 loop : -0.37 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.017 0.001 TYR D 43 PHE 0.017 0.001 PHE C 378 TRP 0.012 0.001 TRP B 382 HIS 0.002 0.000 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00267 (23520) covalent geometry : angle 0.59156 (31892) hydrogen bonds : bond 0.03478 ( 1177) hydrogen bonds : angle 4.00384 ( 3408) *********************** 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 492 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 473 time to evaluate : 0.782 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: 0.8159 (m-80) cc_final: 0.7701 (m-80) REVERT: A 88 ARG cc_start: 0.7277 (ttm170) cc_final: 0.6960 (mtm-85) REVERT: A 90 LYS cc_start: 0.7191 (tppp) cc_final: 0.6866 (tmmt) REVERT: A 103 TYR cc_start: 0.7857 (t80) cc_final: 0.7575 (t80) REVERT: A 190 ASP cc_start: 0.8587 (m-30) cc_final: 0.8310 (m-30) REVERT: A 210 ARG cc_start: 0.7181 (ttt-90) cc_final: 0.6956 (mtp-110) REVERT: A 269 ARG cc_start: 0.5838 (mmm160) cc_final: 0.5548 (mmt-90) REVERT: A 322 MET cc_start: 0.6766 (mmm) cc_final: 0.6483 (mmm) REVERT: A 365 LYS cc_start: 0.7516 (mptt) cc_final: 0.7096 (mppt) REVERT: A 513 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7129 (mtm180) REVERT: A 683 MET cc_start: 0.8550 (tpt) cc_final: 0.8111 (tpt) REVERT: D 55 TYR cc_start: 0.8187 (m-80) cc_final: 0.7581 (m-80) REVERT: D 88 ARG cc_start: 0.7256 (ttm170) cc_final: 0.6944 (mtm-85) REVERT: D 90 LYS cc_start: 0.7194 (tppp) cc_final: 0.6893 (tmmt) REVERT: D 103 TYR cc_start: 0.7839 (t80) cc_final: 0.7564 (t80) REVERT: D 190 ASP cc_start: 0.8592 (m-30) cc_final: 0.8320 (m-30) REVERT: D 210 ARG cc_start: 0.7129 (mtp85) cc_final: 0.6802 (mtp-110) REVERT: D 269 ARG cc_start: 0.5987 (mmm160) cc_final: 0.5417 (mmt180) REVERT: D 365 LYS cc_start: 0.7528 (mptt) cc_final: 0.7113 (mppt) REVERT: D 513 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7137 (mtm180) REVERT: D 683 MET cc_start: 0.8562 (tpt) cc_final: 0.8110 (tpt) REVERT: B 55 TYR cc_start: 0.8167 (m-80) cc_final: 0.7602 (m-80) REVERT: B 88 ARG cc_start: 0.7331 (ttm170) cc_final: 0.6996 (mtm-85) REVERT: B 90 LYS cc_start: 0.7181 (tppp) cc_final: 0.6894 (tmmt) REVERT: B 190 ASP cc_start: 0.8572 (m-30) cc_final: 0.8297 (m-30) REVERT: B 210 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6882 (mtp-110) REVERT: B 246 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7120 (mmt-90) REVERT: B 269 ARG cc_start: 0.6007 (mmm160) cc_final: 0.5424 (mmt180) REVERT: B 349 MET cc_start: 0.7749 (mmt) cc_final: 0.7523 (mmt) REVERT: B 365 LYS cc_start: 0.7546 (mptt) cc_final: 0.7110 (mppt) REVERT: B 391 GLN cc_start: 0.7765 (tt0) cc_final: 0.7448 (tt0) REVERT: B 513 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7125 (mtm180) REVERT: C 55 TYR cc_start: 0.8085 (m-80) cc_final: 0.7710 (m-80) REVERT: C 88 ARG cc_start: 0.7343 (ttm170) cc_final: 0.6982 (mtm-85) REVERT: C 90 LYS cc_start: 0.7163 (tppp) cc_final: 0.6860 (tmmt) REVERT: C 103 TYR cc_start: 0.7839 (t80) cc_final: 0.7561 (t80) REVERT: C 190 ASP cc_start: 0.8575 (m-30) cc_final: 0.8313 (m-30) REVERT: C 197 GLN cc_start: 0.6993 (tt0) cc_final: 0.6187 (mt0) REVERT: C 246 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.6901 (mmt90) REVERT: C 322 MET cc_start: 0.6808 (mmm) cc_final: 0.6511 (mmm) REVERT: C 365 LYS cc_start: 0.7512 (mptt) cc_final: 0.7050 (mppt) REVERT: C 513 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7120 (mtm180) REVERT: C 683 MET cc_start: 0.8563 (tpt) cc_final: 0.8114 (tpt) REVERT: C 691 ARG cc_start: 0.7447 (ptp-170) cc_final: 0.7235 (ptm-80) outliers start: 19 outliers final: 16 residues processed: 483 average time/residue: 0.6848 time to fit residues: 394.9488 Evaluate side-chains 489 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 471 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 448 GLN 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 246 ARG Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 448 GLN 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 246 ARG Chi-restraints excluded: chain C residue 291 THR 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 39 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 280 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 260 optimal weight: 0.2980 overall best weight: 0.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 ASN ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.155638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.124199 restraints weight = 76084.852| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.85 r_work: 0.3097 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2972 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2972 r_free = 0.2972 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2972 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3223 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= 0.137 Angle : 0.602 6.338 31892 Z= 0.281 Chirality : 0.041 0.148 3580 Planarity : 0.003 0.079 4040 Dihedral : 9.227 129.811 3568 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.88 % Allowed : 17.37 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.16), residues: 2956 helix: 2.36 (0.13), residues: 1496 sheet: -0.04 (0.23), residues: 476 loop : -0.41 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 210 TYR 0.018 0.001 TYR D 43 PHE 0.017 0.001 PHE A 378 TRP 0.011 0.001 TRP B 382 HIS 0.002 0.001 HIS C 211 Details of bonding type rmsd covalent geometry : bond 0.00306 (23520) covalent geometry : angle 0.60155 (31892) hydrogen bonds : bond 0.03587 ( 1177) hydrogen bonds : angle 4.02480 ( 3408) ********************** 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 487 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 466 time to evaluate : 0.668 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: 0.8162 (m-80) cc_final: 0.7715 (m-80) REVERT: A 88 ARG cc_start: 0.7318 (ttm170) cc_final: 0.7004 (mtm-85) REVERT: A 90 LYS cc_start: 0.7200 (tppp) cc_final: 0.6909 (tmmt) REVERT: A 190 ASP cc_start: 0.8566 (m-30) cc_final: 0.8310 (m-30) REVERT: A 322 MET cc_start: 0.6797 (mmm) cc_final: 0.6513 (mmm) REVERT: A 365 LYS cc_start: 0.7556 (mptt) cc_final: 0.7122 (mppt) REVERT: D 55 TYR cc_start: 0.8184 (m-80) cc_final: 0.7594 (m-80) REVERT: D 88 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6980 (mtm-85) REVERT: D 90 LYS cc_start: 0.7205 (tppp) cc_final: 0.6919 (tmmt) REVERT: D 190 ASP cc_start: 0.8582 (m-30) cc_final: 0.8329 (m-30) REVERT: D 210 ARG cc_start: 0.7145 (mtp85) cc_final: 0.6814 (mtp-110) REVERT: D 319 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: D 365 LYS cc_start: 0.7548 (mptt) cc_final: 0.7133 (mppt) REVERT: D 513 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7140 (mtm180) REVERT: B 55 TYR cc_start: 0.8170 (m-80) cc_final: 0.7740 (m-80) REVERT: B 88 ARG cc_start: 0.7340 (ttm170) cc_final: 0.7010 (mtm-85) REVERT: B 90 LYS cc_start: 0.7196 (tppp) cc_final: 0.6910 (tmmt) REVERT: B 190 ASP cc_start: 0.8581 (m-30) cc_final: 0.8329 (m-30) REVERT: B 210 ARG cc_start: 0.7232 (mtp85) cc_final: 0.6916 (mtp-110) REVERT: B 246 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7113 (mmt-90) REVERT: B 365 LYS cc_start: 0.7570 (mptt) cc_final: 0.7126 (mppt) REVERT: B 513 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7157 (mtm180) REVERT: C 55 TYR cc_start: 0.8070 (m-80) cc_final: 0.7701 (m-80) REVERT: C 90 LYS cc_start: 0.7171 (tppp) cc_final: 0.6881 (tmmt) REVERT: C 190 ASP cc_start: 0.8560 (m-30) cc_final: 0.8300 (m-30) REVERT: C 246 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.6938 (mmt90) REVERT: C 322 MET cc_start: 0.6807 (mmm) cc_final: 0.6528 (mmm) REVERT: C 349 MET cc_start: 0.7632 (mmt) cc_final: 0.7336 (mmm) REVERT: C 513 ARG cc_start: 0.7625 (mtp-110) cc_final: 0.7133 (mtm180) REVERT: C 691 ARG cc_start: 0.7442 (ptp-170) cc_final: 0.7238 (ptm-80) outliers start: 21 outliers final: 16 residues processed: 476 average time/residue: 0.6434 time to fit residues: 368.3739 Evaluate side-chains 484 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 465 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 GLU Chi-restraints excluded: chain D residue 448 GLN 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 246 ARG Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 448 GLN 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 246 ARG Chi-restraints excluded: chain C residue 291 THR 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 179 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 209 optimal weight: 0.3980 chunk 214 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN C 126 ASN C 211 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.156098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124670 restraints weight = 76031.340| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.85 r_work: 0.3104 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23520 Z= 0.128 Angle : 0.593 6.591 31892 Z= 0.276 Chirality : 0.041 0.146 3580 Planarity : 0.003 0.081 4040 Dihedral : 8.961 127.897 3568 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.84 % Allowed : 17.58 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.16), residues: 2956 helix: 2.41 (0.14), residues: 1496 sheet: -0.01 (0.23), residues: 476 loop : -0.38 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 210 TYR 0.018 0.001 TYR D 43 PHE 0.014 0.001 PHE C 378 TRP 0.012 0.001 TRP D 382 HIS 0.002 0.000 HIS B 733 Details of bonding type rmsd covalent geometry : bond 0.00285 (23520) covalent geometry : angle 0.59296 (31892) hydrogen bonds : bond 0.03492 ( 1177) hydrogen bonds : angle 3.98244 ( 3408) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13126.71 seconds wall clock time: 222 minutes 29.90 seconds (13349.90 seconds total)