Starting phenix.real_space_refine on Sun Jun 29 21:40:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.map" model { file = "/net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fcn_28987/06_2025/8fcn_28987.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 186 5.16 5 C 21942 2.51 5 N 6168 2.21 5 O 6714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 35034 Number of models: 1 Model: "" Number of chains: 18 Chain: "L" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "K" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "J" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "I" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "H" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 145 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.10, per 1000 atoms: 0.57 Number of scatterers: 35034 At special positions: 0 Unit cell: (182.646, 170.97, 97.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 186 16.00 P 24 15.00 O 6714 8.00 N 6168 7.00 C 21942 6.00 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: 8.60 Conformation dependent library (CDL) restraints added in 4.3 seconds 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8316 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 36 sheets defined 52.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'L' and resid 49 through 68 Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 85 through 93 Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.493A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.980A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.513A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 318 through 334 Processing helix chain 'F' and resid 335 through 337 No H-bonds generated for 'chain 'F' and resid 335 through 337' Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 384 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 431 removed outlier: 4.326A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 506 removed outlier: 3.913A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.118A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 612 through 615 Processing helix chain 'F' and resid 625 through 629 Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 649 through 661 Processing helix chain 'F' and resid 671 through 679 Processing helix chain 'F' and resid 683 through 706 removed outlier: 3.702A pdb=" N GLU F 706 " --> pdb=" O SER F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 740 Processing helix chain 'F' and resid 748 through 762 Processing helix chain 'K' and resid 50 through 68 Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.516A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.933A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.518A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 318 through 334 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 431 removed outlier: 4.296A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 506 removed outlier: 3.925A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.127A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 612 through 615 Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 706 removed outlier: 3.695A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 740 removed outlier: 3.526A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 Processing helix chain 'J' and resid 50 through 68 Processing helix chain 'D' and resid 42 through 49 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 209 through 226 removed outlier: 4.486A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 231 removed outlier: 3.973A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.514A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 318 through 334 Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 431 removed outlier: 4.310A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.690A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.129A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 612 through 615 Processing helix chain 'D' and resid 625 through 629 Processing helix chain 'D' and resid 630 through 635 Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 706 removed outlier: 3.690A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'I' and resid 50 through 68 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 85 through 93 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.529A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 231 removed outlier: 3.929A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 318 through 334 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 407 through 431 removed outlier: 4.336A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.850A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.130A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 612 through 615 Processing helix chain 'C' and resid 625 through 629 Processing helix chain 'C' and resid 630 through 635 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 706 removed outlier: 3.698A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 748 through 762 Processing helix chain 'H' and resid 50 through 68 Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.497A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.951A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.517A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 334 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 407 through 431 removed outlier: 4.299A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 444 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.897A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.128A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 612 through 615 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 706 removed outlier: 3.692A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 748 through 762 Processing helix chain 'G' and resid 50 through 68 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.486A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.924A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.506A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 334 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 407 through 431 removed outlier: 4.319A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.854A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.121A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 612 through 615 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 706 removed outlier: 3.698A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 removed outlier: 3.525A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 762 Processing sheet with id=AA1, first strand: chain 'F' and resid 25 through 30 Processing sheet with id=AA2, first strand: chain 'F' and resid 151 through 156 removed outlier: 5.391A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'F' and resid 265 through 270 removed outlier: 6.205A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 469 through 470 removed outlier: 3.611A pdb=" N GLU F 470 " --> pdb=" O PHE F 539 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 25 through 29 Processing sheet with id=AA8, first strand: chain 'E' and resid 151 through 156 removed outlier: 5.374A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 270 removed outlier: 6.202A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.618A pdb=" N GLU E 470 " --> pdb=" O PHE E 539 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 29 Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156 removed outlier: 5.353A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB7, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.195A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 469 through 470 removed outlier: 3.616A pdb=" N GLU D 470 " --> pdb=" O PHE D 539 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 514 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR D 623 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 516 " --> pdb=" O THR D 623 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 25 through 29 Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 156 removed outlier: 5.343A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 126 through 127 Processing sheet with id=AC4, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.783A pdb=" N ARG C 144 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.195A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 469 through 470 removed outlier: 3.613A pdb=" N GLU C 470 " --> pdb=" O PHE C 539 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 25 through 29 Processing sheet with id=AC8, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.347A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 126 through 127 Processing sheet with id=AD1, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'B' and resid 265 through 270 removed outlier: 6.188A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.615A pdb=" N GLU B 470 " --> pdb=" O PHE B 539 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B 514 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 623 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE B 516 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 25 through 29 Processing sheet with id=AD5, first strand: chain 'A' and resid 151 through 156 removed outlier: 5.427A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 167 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 126 through 127 Processing sheet with id=AD7, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AD8, first strand: chain 'A' and resid 265 through 270 removed outlier: 6.201A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.614A pdb=" N GLU A 470 " --> pdb=" O PHE A 539 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 514 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N THR A 623 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE A 516 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) 1678 hydrogen bonds defined for protein. 4692 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: 14.95 Time building geometry restraints manager: 10.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7205 1.33 - 1.45: 7383 1.45 - 1.57: 20680 1.57 - 1.69: 36 1.69 - 1.81: 300 Bond restraints: 35604 Sorted by residual: bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 35599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 47298 2.47 - 4.94: 732 4.94 - 7.41: 72 7.41 - 9.88: 30 9.88 - 12.35: 6 Bond angle restraints: 48138 Sorted by residual: angle pdb=" N ILE C 590 " pdb=" CA ILE C 590 " pdb=" C ILE C 590 " ideal model delta sigma weight residual 111.56 106.66 4.90 8.60e-01 1.35e+00 3.25e+01 angle pdb=" N ILE E 590 " pdb=" CA ILE E 590 " pdb=" C ILE E 590 " ideal model delta sigma weight residual 111.56 106.68 4.88 8.60e-01 1.35e+00 3.22e+01 angle pdb=" N ILE B 590 " pdb=" CA ILE B 590 " pdb=" C ILE B 590 " ideal model delta sigma weight residual 111.56 106.69 4.87 8.60e-01 1.35e+00 3.21e+01 angle pdb=" N ILE D 590 " pdb=" CA ILE D 590 " pdb=" C ILE D 590 " ideal model delta sigma weight residual 111.56 106.70 4.86 8.60e-01 1.35e+00 3.19e+01 angle pdb=" N ILE A 590 " pdb=" CA ILE A 590 " pdb=" C ILE A 590 " ideal model delta sigma weight residual 111.56 106.71 4.85 8.60e-01 1.35e+00 3.18e+01 ... (remaining 48133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 21767 35.98 - 71.97: 235 71.97 - 107.95: 42 107.95 - 143.93: 18 143.93 - 179.92: 6 Dihedral angle restraints: 22068 sinusoidal: 9258 harmonic: 12810 Sorted by residual: dihedral pdb=" O2A ADP D 901 " pdb=" O3A ADP D 901 " pdb=" PA ADP D 901 " pdb=" PB ADP D 901 " ideal model delta sinusoidal sigma weight residual 300.00 120.09 179.92 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PA ADP E 901 " pdb=" PB ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 120.09 179.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 119.74 -179.74 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 22065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3941 0.048 - 0.096: 875 0.096 - 0.144: 468 0.144 - 0.191: 146 0.191 - 0.239: 12 Chirality restraints: 5442 Sorted by residual: chirality pdb=" CA ILE C 590 " pdb=" N ILE C 590 " pdb=" C ILE C 590 " pdb=" CB ILE C 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA ILE E 590 " pdb=" N ILE E 590 " pdb=" C ILE E 590 " pdb=" CB ILE E 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE D 590 " pdb=" N ILE D 590 " pdb=" C ILE D 590 " pdb=" CB ILE D 590 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 5439 not shown) Planarity restraints: 6312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 360 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C PHE C 360 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE C 360 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY C 361 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE F 360 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C PHE F 360 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE F 360 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY F 361 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 360 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C PHE B 360 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE B 360 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 361 " 0.012 2.00e-02 2.50e+03 ... (remaining 6309 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 13327 2.90 - 3.40: 33996 3.40 - 3.90: 60355 3.90 - 4.40: 67758 4.40 - 4.90: 111683 Nonbonded interactions: 287119 Sorted by model distance: nonbonded pdb=" OE2 GLU C 30 " pdb=" NZ LYS C 217 " model vdw 2.403 3.120 nonbonded pdb=" OE2 GLU B 30 " pdb=" NZ LYS B 217 " model vdw 2.412 3.120 nonbonded pdb=" OE2 GLU D 30 " pdb=" NZ LYS D 217 " model vdw 2.432 3.120 nonbonded pdb=" OE2 GLU A 30 " pdb=" NZ LYS A 217 " model vdw 2.435 3.120 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 217 " model vdw 2.437 3.120 ... (remaining 287114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.510 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 78.490 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.200 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:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 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 : 0.010 0.112 35604 Z= 0.588 Angle : 0.816 12.350 48138 Z= 0.498 Chirality : 0.057 0.239 5442 Planarity : 0.003 0.042 6312 Dihedral : 12.732 179.915 13752 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.20 % Favored : 98.66 % Rotamer: Outliers : 0.11 % Allowed : 0.40 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 4410 helix: -0.26 (0.10), residues: 2052 sheet: 0.28 (0.16), residues: 828 loop : 0.95 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 454 HIS 0.001 0.000 HIS B 735 PHE 0.007 0.001 PHE D 575 TYR 0.013 0.001 TYR D 244 ARG 0.002 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.21256 ( 1678) hydrogen bonds : angle 6.45545 ( 4692) covalent geometry : bond 0.01049 (35604) covalent geometry : angle 0.81601 (48138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 834 time to evaluate : 3.966 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: 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 outliers start: 4 outliers final: 6 residues processed: 838 average time/residue: 1.9683 time to fit residues: 1891.1187 Evaluate side-chains 405 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 399 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain A residue 30 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 6.9990 chunk 336 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 348 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 403 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN E 406 HIS E 602 ASN ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN B 90 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.089652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060677 restraints weight = 100304.237| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.35 r_work: 0.2899 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35604 Z= 0.153 Angle : 0.756 10.054 48138 Z= 0.362 Chirality : 0.047 0.210 5442 Planarity : 0.005 0.058 6312 Dihedral : 11.863 172.214 4956 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.69 % Allowed : 10.97 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.12), residues: 4410 helix: 1.18 (0.11), residues: 2040 sheet: 0.69 (0.18), residues: 732 loop : 1.26 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 551 HIS 0.003 0.001 HIS A 317 PHE 0.011 0.001 PHE C 267 TYR 0.022 0.002 TYR D 244 ARG 0.021 0.001 ARG C 599 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 1678) hydrogen bonds : angle 4.63960 ( 4692) covalent geometry : bond 0.00340 (35604) covalent geometry : angle 0.75615 (48138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 476 time to evaluate : 4.001 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: F 239 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7434 (mtt-85) REVERT: F 275 MET cc_start: 0.9497 (mmp) cc_final: 0.9244 (mmp) REVERT: F 304 ASP cc_start: 0.8680 (p0) cc_final: 0.7609 (p0) REVERT: F 335 LEU cc_start: 0.9324 (mt) cc_final: 0.8884 (mt) REVERT: F 354 ASP cc_start: 0.9391 (t0) cc_final: 0.9166 (t0) REVERT: F 489 LEU cc_start: 0.9686 (mt) cc_final: 0.9457 (mp) REVERT: F 554 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8814 (mm-30) REVERT: F 561 GLU cc_start: 0.8699 (mp0) cc_final: 0.8440 (mp0) REVERT: F 565 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9285 (ttpp) REVERT: F 599 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7806 (ttm110) REVERT: F 754 LYS cc_start: 0.9531 (mmpt) cc_final: 0.9326 (ptmm) REVERT: E 84 MET cc_start: 0.8918 (ptt) cc_final: 0.8565 (ptt) REVERT: E 427 MET cc_start: 0.8742 (tpp) cc_final: 0.8519 (tpp) REVERT: E 450 ASP cc_start: 0.9544 (m-30) cc_final: 0.9285 (p0) REVERT: E 470 GLU cc_start: 0.9044 (pt0) cc_final: 0.8843 (pm20) REVERT: E 561 GLU cc_start: 0.8891 (mp0) cc_final: 0.8673 (mp0) REVERT: E 564 ASP cc_start: 0.9474 (t0) cc_final: 0.9272 (t0) REVERT: E 616 ASN cc_start: 0.8671 (t0) cc_final: 0.8090 (p0) REVERT: E 740 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6491 (ptm) REVERT: E 754 LYS cc_start: 0.9579 (mmpt) cc_final: 0.9376 (mmtm) REVERT: D 84 MET cc_start: 0.8872 (ptt) cc_final: 0.8659 (ppp) REVERT: D 134 TYR cc_start: 0.9126 (m-80) cc_final: 0.8870 (m-80) REVERT: D 244 TYR cc_start: 0.8883 (p90) cc_final: 0.8553 (p90) REVERT: D 309 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9123 (mm) REVERT: D 561 GLU cc_start: 0.8899 (mp0) cc_final: 0.8643 (mp0) REVERT: C 64 ARG cc_start: 0.8658 (tpm170) cc_final: 0.8413 (tpm170) REVERT: C 84 MET cc_start: 0.8931 (ptt) cc_final: 0.8665 (ppp) REVERT: C 124 GLU cc_start: 0.9455 (tt0) cc_final: 0.9169 (mp0) REVERT: C 244 TYR cc_start: 0.8900 (p90) cc_final: 0.8629 (p90) REVERT: C 275 MET cc_start: 0.9482 (mmp) cc_final: 0.9218 (mmp) REVERT: C 304 ASP cc_start: 0.8690 (p0) cc_final: 0.7610 (p0) REVERT: C 349 ARG cc_start: 0.8792 (mpp80) cc_final: 0.8553 (mpp80) REVERT: C 354 ASP cc_start: 0.9407 (t0) cc_final: 0.9087 (t0) REVERT: C 561 GLU cc_start: 0.8836 (mp0) cc_final: 0.8558 (mp0) REVERT: C 565 LYS cc_start: 0.9565 (OUTLIER) cc_final: 0.9317 (ttpp) REVERT: C 616 ASN cc_start: 0.8542 (t0) cc_final: 0.8073 (p0) REVERT: C 754 LYS cc_start: 0.9592 (mmpt) cc_final: 0.9350 (mmtm) REVERT: B 64 ARG cc_start: 0.8661 (tpm170) cc_final: 0.8451 (tpm170) REVERT: B 84 MET cc_start: 0.8960 (ptt) cc_final: 0.8667 (ppp) REVERT: B 275 MET cc_start: 0.9457 (mmp) cc_final: 0.9256 (mmp) REVERT: B 305 GLU cc_start: 0.9146 (mp0) cc_final: 0.8677 (mp0) REVERT: B 432 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6662 (pt) REVERT: B 561 GLU cc_start: 0.8870 (mp0) cc_final: 0.8636 (mp0) REVERT: B 616 ASN cc_start: 0.8653 (t0) cc_final: 0.8081 (p0) REVERT: A 134 TYR cc_start: 0.9119 (m-80) cc_final: 0.8894 (m-80) REVERT: A 305 GLU cc_start: 0.9198 (mp0) cc_final: 0.8649 (mp0) REVERT: A 315 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9162 (ptmt) REVERT: A 349 ARG cc_start: 0.8852 (mpp80) cc_final: 0.8613 (mpp80) REVERT: A 560 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8958 (ptm160) REVERT: A 561 GLU cc_start: 0.8964 (mp0) cc_final: 0.8724 (mp0) REVERT: A 565 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9331 (ttpp) outliers start: 101 outliers final: 15 residues processed: 525 average time/residue: 1.7428 time to fit residues: 1072.4675 Evaluate side-chains 397 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 374 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 599 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 740 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 565 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 216 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 303 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 400 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 HIS ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055928 restraints weight = 103550.683| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.29 r_work: 0.2759 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 35604 Z= 0.271 Angle : 0.756 10.113 48138 Z= 0.359 Chirality : 0.046 0.215 5442 Planarity : 0.005 0.076 6312 Dihedral : 10.592 170.659 4938 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.90 % Allowed : 12.14 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.12), residues: 4410 helix: 1.42 (0.11), residues: 2040 sheet: 0.72 (0.18), residues: 732 loop : 1.04 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS E 317 PHE 0.018 0.002 PHE B 230 TYR 0.035 0.003 TYR E 203 ARG 0.008 0.001 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 1678) hydrogen bonds : angle 4.69739 ( 4692) covalent geometry : bond 0.00608 (35604) covalent geometry : angle 0.75569 (48138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 354 time to evaluate : 4.294 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: F 84 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8374 (ppp) REVERT: F 239 ARG cc_start: 0.7997 (mtt90) cc_final: 0.7630 (mtt-85) REVERT: F 305 GLU cc_start: 0.9124 (mp0) cc_final: 0.8866 (mp0) REVERT: F 354 ASP cc_start: 0.9472 (t0) cc_final: 0.9271 (t0) REVERT: F 488 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8602 (mp0) REVERT: F 560 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.9049 (ttt90) REVERT: F 561 GLU cc_start: 0.8818 (mp0) cc_final: 0.8529 (mp0) REVERT: F 564 ASP cc_start: 0.9535 (t0) cc_final: 0.9176 (t0) REVERT: F 616 ASN cc_start: 0.8847 (t0) cc_final: 0.8556 (t0) REVERT: E 84 MET cc_start: 0.8664 (ptt) cc_final: 0.8405 (ppp) REVERT: E 134 TYR cc_start: 0.9273 (m-80) cc_final: 0.9005 (m-80) REVERT: E 244 TYR cc_start: 0.8898 (p90) cc_final: 0.8696 (p90) REVERT: E 305 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8537 (mp0) REVERT: E 354 ASP cc_start: 0.9539 (t0) cc_final: 0.9248 (t0) REVERT: E 427 MET cc_start: 0.8873 (tpp) cc_final: 0.8636 (tpp) REVERT: E 450 ASP cc_start: 0.9583 (m-30) cc_final: 0.9277 (p0) REVERT: E 470 GLU cc_start: 0.9074 (pt0) cc_final: 0.8873 (pm20) REVERT: E 546 GLU cc_start: 0.9248 (tt0) cc_final: 0.8805 (tp30) REVERT: E 561 GLU cc_start: 0.9000 (mp0) cc_final: 0.8630 (mp0) REVERT: E 616 ASN cc_start: 0.8884 (t0) cc_final: 0.8539 (t0) REVERT: D 134 TYR cc_start: 0.9291 (m-80) cc_final: 0.8961 (m-80) REVERT: D 354 ASP cc_start: 0.9558 (t0) cc_final: 0.9332 (t0) REVERT: D 561 GLU cc_start: 0.8966 (mp0) cc_final: 0.8627 (mp0) REVERT: D 564 ASP cc_start: 0.9525 (t0) cc_final: 0.9324 (t0) REVERT: D 616 ASN cc_start: 0.8955 (t0) cc_final: 0.8645 (t0) REVERT: C 64 ARG cc_start: 0.8661 (tpm170) cc_final: 0.8345 (tpm170) REVERT: C 84 MET cc_start: 0.8819 (ptt) cc_final: 0.8593 (ppp) REVERT: C 124 GLU cc_start: 0.9530 (tt0) cc_final: 0.9227 (mp0) REVERT: C 134 TYR cc_start: 0.9116 (m-80) cc_final: 0.8896 (m-80) REVERT: C 304 ASP cc_start: 0.9063 (p0) cc_final: 0.8820 (p0) REVERT: C 305 GLU cc_start: 0.9114 (mp0) cc_final: 0.8801 (mp0) REVERT: C 349 ARG cc_start: 0.8915 (mpp80) cc_final: 0.8713 (mpp80) REVERT: C 561 GLU cc_start: 0.8938 (mp0) cc_final: 0.8551 (mp0) REVERT: C 564 ASP cc_start: 0.9521 (t0) cc_final: 0.9314 (t0) REVERT: C 565 LYS cc_start: 0.9603 (OUTLIER) cc_final: 0.9332 (ttpp) REVERT: C 616 ASN cc_start: 0.8906 (t0) cc_final: 0.8625 (t0) REVERT: B 64 ARG cc_start: 0.8700 (tpm170) cc_final: 0.8426 (tpm170) REVERT: B 84 MET cc_start: 0.8882 (ptt) cc_final: 0.8590 (ppp) REVERT: B 305 GLU cc_start: 0.9069 (mp0) cc_final: 0.8788 (mp0) REVERT: B 354 ASP cc_start: 0.9468 (t0) cc_final: 0.9175 (t0) REVERT: B 442 MET cc_start: 0.9385 (mpp) cc_final: 0.9046 (pmm) REVERT: B 450 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8778 (p0) REVERT: B 546 GLU cc_start: 0.9252 (tt0) cc_final: 0.8747 (tp30) REVERT: B 561 GLU cc_start: 0.8959 (mp0) cc_final: 0.8589 (mp0) REVERT: B 616 ASN cc_start: 0.8868 (t0) cc_final: 0.8514 (t0) REVERT: A 84 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8531 (ppp) REVERT: A 134 TYR cc_start: 0.9308 (m-80) cc_final: 0.9019 (m-80) REVERT: A 244 TYR cc_start: 0.8818 (OUTLIER) cc_final: 0.8499 (p90) REVERT: A 354 ASP cc_start: 0.9513 (t0) cc_final: 0.9265 (t0) REVERT: A 368 ASP cc_start: 0.9227 (t70) cc_final: 0.8977 (t0) REVERT: A 465 ARG cc_start: 0.8410 (mtt90) cc_final: 0.8083 (mtt90) REVERT: A 561 GLU cc_start: 0.9014 (mp0) cc_final: 0.8651 (mp0) REVERT: A 616 ASN cc_start: 0.8929 (t0) cc_final: 0.8490 (t0) outliers start: 109 outliers final: 25 residues processed: 424 average time/residue: 1.6847 time to fit residues: 845.2297 Evaluate side-chains 344 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 312 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 670 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 670 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 670 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 303 optimal weight: 9.9990 chunk 373 optimal weight: 8.9990 chunk 412 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 278 optimal weight: 0.9980 chunk 213 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 336 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 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 = 0.3667 r_free = 0.3667 target = 0.086003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056291 restraints weight = 101898.070| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.38 r_work: 0.2802 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 35604 Z= 0.128 Angle : 0.662 9.537 48138 Z= 0.309 Chirality : 0.045 0.204 5442 Planarity : 0.004 0.048 6312 Dihedral : 10.008 158.497 4938 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.37 % Allowed : 13.15 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.13), residues: 4410 helix: 1.59 (0.11), residues: 2052 sheet: 0.81 (0.18), residues: 732 loop : 1.08 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 454 HIS 0.003 0.000 HIS D 340 PHE 0.009 0.001 PHE B 516 TYR 0.028 0.002 TYR C 203 ARG 0.010 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1678) hydrogen bonds : angle 4.34705 ( 4692) covalent geometry : bond 0.00287 (35604) covalent geometry : angle 0.66196 (48138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 4.049 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: F 84 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (ppp) REVERT: F 239 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7602 (mtt-85) REVERT: F 305 GLU cc_start: 0.8995 (mp0) cc_final: 0.8498 (mp0) REVERT: F 335 LEU cc_start: 0.9413 (mt) cc_final: 0.9173 (mt) REVERT: F 354 ASP cc_start: 0.9480 (t0) cc_final: 0.9214 (t0) REVERT: F 488 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8583 (mp0) REVERT: F 560 ARG cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (ttm-80) REVERT: F 561 GLU cc_start: 0.8906 (mp0) cc_final: 0.8582 (mp0) REVERT: F 565 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9369 (ttpp) REVERT: F 616 ASN cc_start: 0.8880 (t0) cc_final: 0.8566 (t0) REVERT: E 84 MET cc_start: 0.8718 (ptt) cc_final: 0.8441 (ppp) REVERT: E 134 TYR cc_start: 0.9287 (m-80) cc_final: 0.8974 (m-80) REVERT: E 305 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8584 (mp0) REVERT: E 354 ASP cc_start: 0.9506 (t0) cc_final: 0.9254 (t0) REVERT: E 432 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7113 (pt) REVERT: E 442 MET cc_start: 0.9436 (mpp) cc_final: 0.8785 (pmm) REVERT: E 450 ASP cc_start: 0.9572 (m-30) cc_final: 0.9241 (t0) REVERT: E 546 GLU cc_start: 0.9218 (tt0) cc_final: 0.8751 (tp30) REVERT: E 561 GLU cc_start: 0.9011 (mp0) cc_final: 0.8600 (mp0) REVERT: E 616 ASN cc_start: 0.8919 (t0) cc_final: 0.8590 (t0) REVERT: D 134 TYR cc_start: 0.9320 (m-80) cc_final: 0.9037 (m-80) REVERT: D 354 ASP cc_start: 0.9566 (t0) cc_final: 0.9237 (t0) REVERT: D 442 MET cc_start: 0.9407 (mpp) cc_final: 0.8742 (pmm) REVERT: D 561 GLU cc_start: 0.8996 (mp0) cc_final: 0.8601 (mp0) REVERT: D 616 ASN cc_start: 0.8976 (t0) cc_final: 0.8676 (t0) REVERT: C 64 ARG cc_start: 0.8595 (tpm170) cc_final: 0.8289 (tpm170) REVERT: C 84 MET cc_start: 0.8795 (ptt) cc_final: 0.8593 (ppp) REVERT: C 124 GLU cc_start: 0.9531 (tt0) cc_final: 0.9174 (mp0) REVERT: C 134 TYR cc_start: 0.9179 (m-80) cc_final: 0.8938 (m-80) REVERT: C 305 GLU cc_start: 0.9003 (mp0) cc_final: 0.8496 (mp0) REVERT: C 349 ARG cc_start: 0.8951 (mpp80) cc_final: 0.8727 (mpp80) REVERT: C 354 ASP cc_start: 0.9426 (t0) cc_final: 0.9124 (t0) REVERT: C 379 GLU cc_start: 0.9408 (mt-10) cc_final: 0.8806 (mt-10) REVERT: C 442 MET cc_start: 0.9392 (mpp) cc_final: 0.8841 (pmm) REVERT: C 561 GLU cc_start: 0.8986 (mp0) cc_final: 0.8544 (mp0) REVERT: C 565 LYS cc_start: 0.9609 (OUTLIER) cc_final: 0.9350 (ttpp) REVERT: C 616 ASN cc_start: 0.8937 (t0) cc_final: 0.8643 (t0) REVERT: B 64 ARG cc_start: 0.8698 (tpm170) cc_final: 0.8356 (tpm170) REVERT: B 84 MET cc_start: 0.8848 (ptt) cc_final: 0.8567 (ppp) REVERT: B 305 GLU cc_start: 0.9068 (mp0) cc_final: 0.8516 (mp0) REVERT: B 354 ASP cc_start: 0.9489 (t0) cc_final: 0.9235 (t0) REVERT: B 442 MET cc_start: 0.9274 (mpp) cc_final: 0.8925 (pmm) REVERT: B 450 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8859 (p0) REVERT: B 546 GLU cc_start: 0.9223 (tt0) cc_final: 0.8762 (tp30) REVERT: B 561 GLU cc_start: 0.8992 (mp0) cc_final: 0.8575 (mp0) REVERT: B 616 ASN cc_start: 0.8873 (t0) cc_final: 0.8535 (t0) REVERT: A 84 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8319 (ppp) REVERT: A 134 TYR cc_start: 0.9319 (m-80) cc_final: 0.8932 (m-80) REVERT: A 173 TYR cc_start: 0.7721 (p90) cc_final: 0.7165 (p90) REVERT: A 315 LYS cc_start: 0.9590 (mmpt) cc_final: 0.9151 (mtmt) REVERT: A 354 ASP cc_start: 0.9499 (t0) cc_final: 0.9248 (t0) REVERT: A 465 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7845 (mtt90) REVERT: A 561 GLU cc_start: 0.9048 (mp0) cc_final: 0.8649 (mp0) REVERT: A 616 ASN cc_start: 0.8982 (t0) cc_final: 0.8679 (t0) outliers start: 89 outliers final: 19 residues processed: 402 average time/residue: 1.6997 time to fit residues: 805.4904 Evaluate side-chains 334 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 560 ARG Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 560 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 223 optimal weight: 10.0000 chunk 199 optimal weight: 0.4980 chunk 211 optimal weight: 0.9980 chunk 322 optimal weight: 0.0980 chunk 289 optimal weight: 1.9990 chunk 278 optimal weight: 0.4980 chunk 252 optimal weight: 0.9990 chunk 288 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 425 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 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 = 0.3685 r_free = 0.3685 target = 0.087610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.058064 restraints weight = 101859.614| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.38 r_work: 0.2825 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35604 Z= 0.115 Angle : 0.662 9.888 48138 Z= 0.306 Chirality : 0.044 0.213 5442 Planarity : 0.004 0.048 6312 Dihedral : 9.542 149.789 4938 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.94 % Allowed : 14.46 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 4410 helix: 1.75 (0.11), residues: 2028 sheet: 0.88 (0.19), residues: 732 loop : 1.00 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 454 HIS 0.002 0.000 HIS D 340 PHE 0.008 0.001 PHE C 52 TYR 0.022 0.002 TYR E 203 ARG 0.018 0.001 ARG B 349 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 1678) hydrogen bonds : angle 4.20277 ( 4692) covalent geometry : bond 0.00257 (35604) covalent geometry : angle 0.66237 (48138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 343 time to evaluate : 4.411 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: F 84 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8276 (ppp) REVERT: F 239 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7550 (mtt-85) REVERT: F 354 ASP cc_start: 0.9449 (t0) cc_final: 0.9200 (t0) REVERT: F 488 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: F 561 GLU cc_start: 0.8929 (mp0) cc_final: 0.8587 (mp0) REVERT: F 616 ASN cc_start: 0.8924 (t0) cc_final: 0.8600 (t0) REVERT: E 84 MET cc_start: 0.8762 (ptt) cc_final: 0.8478 (ppp) REVERT: E 134 TYR cc_start: 0.9297 (m-80) cc_final: 0.8982 (m-80) REVERT: E 305 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8629 (mp0) REVERT: E 354 ASP cc_start: 0.9489 (t0) cc_final: 0.9251 (t0) REVERT: E 432 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.7084 (pt) REVERT: E 442 MET cc_start: 0.9469 (mpp) cc_final: 0.8816 (pmm) REVERT: E 450 ASP cc_start: 0.9549 (m-30) cc_final: 0.9230 (p0) REVERT: E 546 GLU cc_start: 0.9186 (tt0) cc_final: 0.8730 (tp30) REVERT: E 561 GLU cc_start: 0.9010 (mp0) cc_final: 0.8594 (mp0) REVERT: E 616 ASN cc_start: 0.8905 (t0) cc_final: 0.8566 (t0) REVERT: D 134 TYR cc_start: 0.9334 (m-80) cc_final: 0.9031 (m-80) REVERT: D 305 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8490 (mp0) REVERT: D 315 LYS cc_start: 0.9152 (pttt) cc_final: 0.8875 (mppt) REVERT: D 354 ASP cc_start: 0.9447 (t0) cc_final: 0.9127 (t0) REVERT: D 379 GLU cc_start: 0.9470 (mt-10) cc_final: 0.8840 (mt-10) REVERT: D 442 MET cc_start: 0.9429 (mpp) cc_final: 0.9210 (mpp) REVERT: D 561 GLU cc_start: 0.8992 (mp0) cc_final: 0.8598 (mp0) REVERT: C 64 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8235 (tpm170) REVERT: C 124 GLU cc_start: 0.9519 (tt0) cc_final: 0.9152 (mp0) REVERT: C 134 TYR cc_start: 0.9237 (m-80) cc_final: 0.8954 (m-80) REVERT: C 349 ARG cc_start: 0.8972 (mpp80) cc_final: 0.8740 (mpp80) REVERT: C 379 GLU cc_start: 0.9450 (mt-10) cc_final: 0.8822 (mt-10) REVERT: C 442 MET cc_start: 0.9443 (mpp) cc_final: 0.8758 (pmm) REVERT: C 561 GLU cc_start: 0.9005 (mp0) cc_final: 0.8575 (mp0) REVERT: C 564 ASP cc_start: 0.9442 (t0) cc_final: 0.9227 (m-30) REVERT: C 565 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9356 (ttpp) REVERT: B 64 ARG cc_start: 0.8675 (tpm170) cc_final: 0.8320 (tpm170) REVERT: B 84 MET cc_start: 0.8838 (ptt) cc_final: 0.8562 (ppp) REVERT: B 305 GLU cc_start: 0.9062 (mp0) cc_final: 0.8509 (mp0) REVERT: B 354 ASP cc_start: 0.9446 (t0) cc_final: 0.9194 (t0) REVERT: B 442 MET cc_start: 0.9272 (mpp) cc_final: 0.8923 (pmm) REVERT: B 450 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8804 (p0) REVERT: B 546 GLU cc_start: 0.9217 (tt0) cc_final: 0.8753 (tp30) REVERT: B 561 GLU cc_start: 0.9011 (mp0) cc_final: 0.8598 (mp0) REVERT: B 616 ASN cc_start: 0.8868 (t0) cc_final: 0.8520 (t0) REVERT: A 84 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8378 (ppp) REVERT: A 134 TYR cc_start: 0.9332 (m-80) cc_final: 0.9029 (m-80) REVERT: A 143 TYR cc_start: 0.8668 (m-80) cc_final: 0.8401 (m-80) REVERT: A 173 TYR cc_start: 0.7691 (p90) cc_final: 0.7142 (p90) REVERT: A 354 ASP cc_start: 0.9462 (t0) cc_final: 0.9139 (t0) REVERT: A 560 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8761 (ptm160) REVERT: A 561 GLU cc_start: 0.9021 (mp0) cc_final: 0.8649 (mp0) REVERT: A 564 ASP cc_start: 0.9472 (t0) cc_final: 0.9216 (m-30) outliers start: 73 outliers final: 22 residues processed: 381 average time/residue: 1.5986 time to fit residues: 725.5591 Evaluate side-chains 341 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 312 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 560 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 434 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 398 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 377 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054291 restraints weight = 103408.122| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 4.37 r_work: 0.2753 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35604 Z= 0.211 Angle : 0.707 11.026 48138 Z= 0.328 Chirality : 0.045 0.221 5442 Planarity : 0.004 0.051 6312 Dihedral : 9.192 141.676 4938 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.24 % Allowed : 15.04 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.13), residues: 4410 helix: 1.76 (0.12), residues: 2052 sheet: 0.87 (0.19), residues: 732 loop : 0.96 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 476 HIS 0.003 0.001 HIS D 340 PHE 0.011 0.001 PHE B 516 TYR 0.034 0.002 TYR C 203 ARG 0.017 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1678) hydrogen bonds : angle 4.32628 ( 4692) covalent geometry : bond 0.00477 (35604) covalent geometry : angle 0.70708 (48138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 303 time to evaluate : 4.231 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: F 84 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8223 (ppp) REVERT: F 134 TYR cc_start: 0.9180 (m-80) cc_final: 0.8958 (m-80) REVERT: F 354 ASP cc_start: 0.9496 (t0) cc_final: 0.9278 (t0) REVERT: F 488 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8626 (mp0) REVERT: F 561 GLU cc_start: 0.9088 (mp0) cc_final: 0.8636 (mp0) REVERT: F 565 LYS cc_start: 0.9602 (OUTLIER) cc_final: 0.9377 (ttpp) REVERT: F 616 ASN cc_start: 0.8997 (t0) cc_final: 0.8710 (t0) REVERT: F 700 ARG cc_start: 0.9368 (OUTLIER) cc_final: 0.9031 (ttp80) REVERT: E 84 MET cc_start: 0.8674 (ptt) cc_final: 0.8413 (ppp) REVERT: E 134 TYR cc_start: 0.9281 (m-80) cc_final: 0.8997 (m-80) REVERT: E 305 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8569 (mp0) REVERT: E 354 ASP cc_start: 0.9547 (t0) cc_final: 0.9335 (t0) REVERT: E 432 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6863 (pp) REVERT: E 442 MET cc_start: 0.9514 (mpp) cc_final: 0.8873 (pmm) REVERT: E 546 GLU cc_start: 0.9186 (tt0) cc_final: 0.8748 (tp30) REVERT: E 561 GLU cc_start: 0.9049 (mp0) cc_final: 0.8600 (mp0) REVERT: E 616 ASN cc_start: 0.9005 (t0) cc_final: 0.8677 (t0) REVERT: D 134 TYR cc_start: 0.9338 (m-80) cc_final: 0.8957 (m-80) REVERT: D 305 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8584 (mp0) REVERT: D 354 ASP cc_start: 0.9489 (t0) cc_final: 0.9273 (t0) REVERT: D 442 MET cc_start: 0.9508 (mpp) cc_final: 0.8905 (pmm) REVERT: D 561 GLU cc_start: 0.9043 (mp0) cc_final: 0.8615 (mp0) REVERT: D 611 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8516 (ttm) REVERT: D 616 ASN cc_start: 0.9085 (t0) cc_final: 0.8787 (t0) REVERT: C 64 ARG cc_start: 0.8668 (tpm170) cc_final: 0.8186 (tpm170) REVERT: C 124 GLU cc_start: 0.9559 (tt0) cc_final: 0.9153 (mp0) REVERT: C 134 TYR cc_start: 0.9278 (m-80) cc_final: 0.8996 (m-80) REVERT: C 305 GLU cc_start: 0.9064 (mp0) cc_final: 0.8723 (mp0) REVERT: C 442 MET cc_start: 0.9492 (mpp) cc_final: 0.9064 (pmm) REVERT: C 546 GLU cc_start: 0.9238 (tt0) cc_final: 0.8750 (tp30) REVERT: C 561 GLU cc_start: 0.9022 (mp0) cc_final: 0.8546 (mp0) REVERT: C 565 LYS cc_start: 0.9614 (OUTLIER) cc_final: 0.9364 (ttpp) REVERT: C 616 ASN cc_start: 0.9024 (t0) cc_final: 0.8756 (t0) REVERT: C 700 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.9014 (ttp80) REVERT: B 64 ARG cc_start: 0.8774 (tpm170) cc_final: 0.8414 (tpm170) REVERT: B 84 MET cc_start: 0.8815 (ptt) cc_final: 0.8249 (ptt) REVERT: B 305 GLU cc_start: 0.9057 (mp0) cc_final: 0.8542 (mp0) REVERT: B 354 ASP cc_start: 0.9485 (t0) cc_final: 0.9281 (t0) REVERT: B 365 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7615 (mtt90) REVERT: B 442 MET cc_start: 0.9325 (mpp) cc_final: 0.9038 (pmm) REVERT: B 450 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8797 (p0) REVERT: B 546 GLU cc_start: 0.9219 (tt0) cc_final: 0.8772 (tp30) REVERT: B 561 GLU cc_start: 0.9044 (mp0) cc_final: 0.8602 (mp0) REVERT: B 616 ASN cc_start: 0.8977 (t0) cc_final: 0.8640 (t0) REVERT: A 84 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8357 (ppp) REVERT: A 134 TYR cc_start: 0.9339 (m-80) cc_final: 0.9038 (m-80) REVERT: A 143 TYR cc_start: 0.8663 (m-80) cc_final: 0.8369 (m-80) REVERT: A 173 TYR cc_start: 0.7864 (p90) cc_final: 0.7268 (p90) REVERT: A 217 LYS cc_start: 0.9680 (mtmt) cc_final: 0.9379 (mtmm) REVERT: A 315 LYS cc_start: 0.9455 (mmpt) cc_final: 0.9111 (mtmt) REVERT: A 546 GLU cc_start: 0.9223 (tt0) cc_final: 0.8767 (tp30) REVERT: A 561 GLU cc_start: 0.9070 (mp0) cc_final: 0.8629 (mp0) REVERT: A 564 ASP cc_start: 0.9497 (t0) cc_final: 0.9270 (m-30) REVERT: A 611 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8517 (ttm) outliers start: 84 outliers final: 23 residues processed: 355 average time/residue: 1.8713 time to fit residues: 787.8431 Evaluate side-chains 317 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 4.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 462 SER Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain F residue 700 ARG Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain C residue 700 ARG Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 560 ARG Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 560 ARG Chi-restraints excluded: chain A residue 611 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 292 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 380 optimal weight: 6.9990 chunk 395 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.085593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055889 restraints weight = 102695.192| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.36 r_work: 0.2794 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35604 Z= 0.126 Angle : 0.683 10.908 48138 Z= 0.314 Chirality : 0.044 0.215 5442 Planarity : 0.004 0.059 6312 Dihedral : 8.558 128.272 4938 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.94 % Allowed : 15.65 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.13), residues: 4410 helix: 1.84 (0.12), residues: 2034 sheet: 0.92 (0.18), residues: 744 loop : 0.93 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 454 HIS 0.003 0.000 HIS D 340 PHE 0.008 0.001 PHE A 52 TYR 0.014 0.002 TYR F 203 ARG 0.015 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 1678) hydrogen bonds : angle 4.14225 ( 4692) covalent geometry : bond 0.00288 (35604) covalent geometry : angle 0.68277 (48138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8820 Ramachandran restraints generated. 4410 Oldfield, 0 Emsley, 4410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 312 time to evaluate : 6.718 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: F 64 ARG cc_start: 0.8817 (ptp90) cc_final: 0.8600 (mtm-85) REVERT: F 84 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8306 (ppp) REVERT: F 217 LYS cc_start: 0.9642 (mtmt) cc_final: 0.9305 (mtmm) REVERT: F 354 ASP cc_start: 0.9475 (t0) cc_final: 0.9229 (t0) REVERT: F 488 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8652 (mp0) REVERT: F 561 GLU cc_start: 0.9124 (mp0) cc_final: 0.8675 (mp0) REVERT: F 565 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9403 (ttpp) REVERT: F 616 ASN cc_start: 0.8974 (t0) cc_final: 0.8690 (t0) REVERT: E 84 MET cc_start: 0.8748 (ptt) cc_final: 0.8488 (ppp) REVERT: E 134 TYR cc_start: 0.9264 (m-80) cc_final: 0.9008 (m-80) REVERT: E 217 LYS cc_start: 0.9647 (mtmt) cc_final: 0.9348 (mtmm) REVERT: E 305 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8606 (mp0) REVERT: E 379 GLU cc_start: 0.9478 (mt-10) cc_final: 0.8907 (mt-10) REVERT: E 432 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6844 (pp) REVERT: E 442 MET cc_start: 0.9495 (mpp) cc_final: 0.9272 (mpp) REVERT: E 546 GLU cc_start: 0.9179 (tt0) cc_final: 0.8747 (tp30) REVERT: E 561 GLU cc_start: 0.9038 (mp0) cc_final: 0.8599 (mp0) REVERT: E 616 ASN cc_start: 0.8990 (t0) cc_final: 0.8664 (t0) REVERT: D 134 TYR cc_start: 0.9331 (m-80) cc_final: 0.8993 (m-80) REVERT: D 305 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8624 (mp0) REVERT: D 354 ASP cc_start: 0.9458 (t0) cc_final: 0.9112 (t70) REVERT: D 442 MET cc_start: 0.9494 (mpp) cc_final: 0.9261 (mpp) REVERT: D 561 GLU cc_start: 0.9046 (mp0) cc_final: 0.8594 (mp0) REVERT: D 564 ASP cc_start: 0.9428 (m-30) cc_final: 0.9202 (m-30) REVERT: D 616 ASN cc_start: 0.9041 (t0) cc_final: 0.8754 (t0) REVERT: C 64 ARG cc_start: 0.8660 (tpm170) cc_final: 0.8157 (tpm170) REVERT: C 124 GLU cc_start: 0.9535 (tt0) cc_final: 0.9147 (mp0) REVERT: C 134 TYR cc_start: 0.9293 (m-80) cc_final: 0.8970 (m-80) REVERT: C 305 GLU cc_start: 0.9115 (mp0) cc_final: 0.8714 (mp0) REVERT: C 379 GLU cc_start: 0.9458 (mt-10) cc_final: 0.8848 (mt-10) REVERT: C 442 MET cc_start: 0.9481 (mpp) cc_final: 0.8859 (pmm) REVERT: C 546 GLU cc_start: 0.9225 (tt0) cc_final: 0.8798 (tp30) REVERT: C 561 GLU cc_start: 0.9020 (mp0) cc_final: 0.8564 (mp0) REVERT: C 565 LYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9394 (ttpp) REVERT: C 616 ASN cc_start: 0.9010 (t0) cc_final: 0.8732 (t0) REVERT: B 32 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8595 (mp) REVERT: B 46 MET cc_start: 0.8927 (ppp) cc_final: 0.8289 (ppp) REVERT: B 64 ARG cc_start: 0.8719 (tpm170) cc_final: 0.8324 (tpm170) REVERT: B 84 MET cc_start: 0.8854 (ptt) cc_final: 0.8289 (ptt) REVERT: B 305 GLU cc_start: 0.9121 (mp0) cc_final: 0.8684 (mp0) REVERT: B 354 ASP cc_start: 0.9492 (t0) cc_final: 0.9264 (t0) REVERT: B 365 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7249 (mtt90) REVERT: B 442 MET cc_start: 0.9313 (mpp) cc_final: 0.8989 (pmm) REVERT: B 450 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8795 (p0) REVERT: B 488 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8874 (mp0) REVERT: B 546 GLU cc_start: 0.9209 (tt0) cc_final: 0.8776 (tp30) REVERT: B 561 GLU cc_start: 0.9036 (mp0) cc_final: 0.8580 (mp0) REVERT: B 616 ASN cc_start: 0.8975 (t0) cc_final: 0.8644 (t0) REVERT: A 64 ARG cc_start: 0.8871 (mpp-170) cc_final: 0.8663 (mtm-85) REVERT: A 84 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8414 (ppp) REVERT: A 134 TYR cc_start: 0.9323 (m-80) cc_final: 0.8989 (m-80) REVERT: A 173 TYR cc_start: 0.7798 (p90) cc_final: 0.7188 (p90) REVERT: A 217 LYS cc_start: 0.9678 (mtmt) cc_final: 0.9461 (mtpp) REVERT: A 546 GLU cc_start: 0.9202 (tt0) cc_final: 0.8749 (tp30) REVERT: A 560 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8772 (ptm160) REVERT: A 561 GLU cc_start: 0.9087 (mp0) cc_final: 0.8677 (mp0) REVERT: A 564 ASP cc_start: 0.9495 (t0) cc_final: 0.9248 (m-30) outliers start: 73 outliers final: 22 residues processed: 353 average time/residue: 1.9475 time to fit residues: 811.4185 Evaluate side-chains 327 residues out of total 3756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 4.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 488 GLU Chi-restraints excluded: chain F residue 565 LYS Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 565 LYS Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 244 TYR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 450 ASP Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 560 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.8902 > 50: distance: 68 - 72: 27.757 distance: 72 - 73: 24.243 distance: 73 - 74: 21.078 distance: 73 - 76: 22.441 distance: 74 - 75: 19.523 distance: 74 - 77: 15.859 distance: 77 - 78: 13.525 distance: 78 - 79: 20.745 distance: 78 - 81: 37.969 distance: 79 - 80: 22.970 distance: 79 - 85: 20.604 distance: 81 - 82: 57.229 distance: 81 - 83: 57.576 distance: 82 - 84: 40.749 distance: 85 - 86: 22.283 distance: 86 - 87: 8.199 distance: 87 - 88: 14.027 distance: 87 - 89: 17.597 distance: 89 - 90: 9.286 distance: 90 - 91: 13.665 distance: 90 - 93: 8.743 distance: 91 - 92: 41.012 distance: 91 - 96: 54.015 distance: 93 - 94: 28.365 distance: 93 - 95: 32.193 distance: 96 - 97: 61.890 distance: 97 - 98: 26.399 distance: 97 - 100: 43.269 distance: 98 - 99: 35.574 distance: 98 - 105: 31.111 distance: 100 - 101: 21.383 distance: 101 - 102: 18.049 distance: 102 - 103: 22.419 distance: 103 - 104: 21.057 distance: 105 - 106: 34.006 distance: 105 - 111: 14.639 distance: 106 - 107: 47.694 distance: 106 - 109: 37.700 distance: 107 - 112: 50.492 distance: 109 - 110: 3.158 distance: 110 - 111: 36.256 distance: 112 - 113: 28.896 distance: 112 - 118: 19.811 distance: 113 - 114: 19.204 distance: 113 - 116: 8.659 distance: 114 - 115: 8.757 distance: 114 - 119: 41.342 distance: 116 - 117: 35.180 distance: 117 - 118: 31.401 distance: 119 - 120: 27.225 distance: 120 - 121: 13.750 distance: 120 - 123: 51.330 distance: 121 - 122: 14.186 distance: 121 - 130: 51.508 distance: 123 - 124: 48.927 distance: 124 - 125: 47.029 distance: 125 - 126: 16.044 distance: 126 - 127: 5.553 distance: 127 - 128: 20.907 distance: 127 - 129: 20.831 distance: 130 - 131: 44.512 distance: 131 - 132: 17.008 distance: 132 - 133: 32.913 distance: 132 - 134: 18.336 distance: 133 - 212: 9.328 distance: 134 - 135: 8.221 distance: 134 - 178: 25.313 distance: 135 - 136: 44.733 distance: 135 - 138: 15.824 distance: 136 - 137: 15.566 distance: 136 - 142: 19.505 distance: 137 - 190: 25.424 distance: 138 - 139: 39.672 distance: 138 - 140: 10.678 distance: 139 - 141: 28.354