Starting phenix.real_space_refine on Fri Jul 3 19:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.cif Found real_map, /net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7at8_11910/07_2026/7at8_11910.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 7 6.06 5 P 310 5.49 5 S 55 5.16 5 C 9053 2.51 5 N 2945 2.21 5 O 3581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15951 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 619 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain breaks: 4 Chain: "A" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1851 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 13, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1024 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "E" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "F" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "I" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "J" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3176 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "U" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3214 Classifications: {'DNA': 156} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 155} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 33 Unusual residues: {' ZN': 7} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 222 SG CYS A 286 42.792 44.930 98.704 1.00172.70 S ATOM 250 SG CYS A 289 39.019 44.911 98.087 0.99172.87 S ATOM 296 SG CYS A 294 41.047 41.721 97.546 0.87165.55 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 958 SG CYS A 567 55.456 57.195 95.986 1.00196.50 S ATOM 985 SG CYS A 571 57.977 58.482 93.473 1.00189.83 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 815 SG CYS A 548 59.081 55.951 95.973 1.00224.51 S ATOM 841 SG CYS A 552 60.285 52.403 95.140 1.00211.70 S ATOM 760 SG CYS A 541 56.817 52.987 96.687 1.00200.99 S ATOM 854 SG CYS A 554 56.701 51.050 93.445 0.93198.28 S ATOM 908 SG CYS A 561 56.647 54.817 93.302 1.00185.75 S ATOM 943 SG CYS A 565 53.618 52.936 94.782 1.00180.30 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1255 SG CYS A 606 40.534 60.860 80.840 1.00151.54 S ATOM 1351 SG CYS A 619 39.256 57.835 79.458 1.00148.68 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1139 SG CYS A 591 46.636 58.342 81.480 1.00155.72 S ATOM 1197 SG CYS A 598 42.846 57.761 80.573 1.00148.79 S ATOM 1234 SG CYS A 603 44.045 59.728 83.596 1.00143.87 S ATOM 1041 SG CYS A 578 44.356 61.108 80.066 1.00152.37 S ATOM 1058 SG CYS A 580 44.717 62.660 76.821 1.00142.11 S ATOM 1087 SG CYS A 584 42.028 59.705 77.412 1.00141.94 S ATOM 1126 SG CYS A 589 45.819 59.144 77.101 1.00147.49 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALA D 31 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA D 31 " occ=0.00 residue: pdb=" N THR D 32 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR D 32 " occ=0.00 Time building chain proxies: 2.53, per 1000 atoms: 0.16 Number of scatterers: 15951 At special positions: 0 Unit cell: (130.95, 171.108, 144.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 7 29.99 S 55 16.00 P 310 15.00 O 3581 8.00 N 2945 7.00 C 9053 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: 1.05 Conformation dependent library (CDL) restraints added in 501.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 297 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 289 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 286 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 294 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 567 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 571 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 561 " pdb=" ZN A1003 " pdb="ZN ZN A1003 " - pdb=" NE2 HIS A 543 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 548 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1003 " - pdb=" SG CYS A 552 " pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 541 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 554 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 565 " pdb=" ZN A1005 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 619 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 606 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1005 " - pdb=" SG CYS A 584 " pdb=" ZN A1006 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 603 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 598 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1006 " - pdb=" SG CYS A 591 " pdb=" ZN A1007 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 578 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 589 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 580 " pdb="ZN ZN A1007 " - pdb=" SG CYS A 584 " Number of angles added : 36 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 13 sheets defined 61.0% alpha, 4.7% beta 150 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 144 through 153 removed outlier: 3.521A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 removed outlier: 3.736A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 462 removed outlier: 3.673A pdb=" N ARG A 461 " --> pdb=" O CYS A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 493 through 504 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 589 through 594 Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 666 through 679 removed outlier: 3.545A pdb=" N ASP A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'C' and resid 589 through 602 removed outlier: 4.055A pdb=" N ARG C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU C 594 " --> pdb=" O GLU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 625 removed outlier: 4.377A pdb=" N MET C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 650 removed outlier: 4.426A pdb=" N HIS C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 640 " --> pdb=" O CYS C 636 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS C 646 " --> pdb=" O ASN C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 666 Processing helix chain 'C' and resid 671 through 684 removed outlier: 3.920A pdb=" N ASP C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.878A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 131 Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.693A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.479A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 93 removed outlier: 3.950A pdb=" N VAL E 86 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.685A pdb=" N VAL F 30 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 73 removed outlier: 4.538A pdb=" N VAL F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 90 removed outlier: 3.553A pdb=" N ASP F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 97 Processing helix chain 'G' and resid 34 through 46 Processing helix chain 'G' and resid 52 through 81 Processing helix chain 'G' and resid 87 through 99 removed outlier: 3.563A pdb=" N ILE G 91 " --> pdb=" O THR G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 121 removed outlier: 3.863A pdb=" N ALA G 121 " --> pdb=" O LYS G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 57 Processing helix chain 'H' and resid 63 through 79 removed outlier: 3.943A pdb=" N PHE H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 114 Processing helix chain 'H' and resid 120 through 131 Processing helix chain 'I' and resid 25 through 29 removed outlier: 3.704A pdb=" N ILE I 29 " --> pdb=" O ILE I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 42 Processing helix chain 'I' and resid 49 through 76 removed outlier: 4.390A pdb=" N GLU I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.920A pdb=" N VAL I 86 " --> pdb=" O THR I 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 22 Processing helix chain 'J' and resid 26 through 37 removed outlier: 3.623A pdb=" N VAL J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 73 Processing helix chain 'J' and resid 79 through 90 removed outlier: 3.669A pdb=" N ASP J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 52 through 81 Processing helix chain 'K' and resid 87 through 99 removed outlier: 3.591A pdb=" N ILE K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 121 removed outlier: 3.817A pdb=" N ALA K 121 " --> pdb=" O LYS K 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.761A pdb=" N SER A 114 " --> pdb=" O GLY A 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 removed outlier: 6.204A pdb=" N PHE A 120 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER A 665 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286 Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 636 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658 removed outlier: 6.780A pdb=" N PHE A 655 " --> pdb=" O ALA A 730 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 730 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.991A pdb=" N ARG D 83 " --> pdb=" O VAL E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'F' and resid 42 through 43 removed outlier: 7.645A pdb=" N ARG F 42 " --> pdb=" O ILE G 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78 removed outlier: 3.648A pdb=" N ILE F 78 " --> pdb=" O GLY G 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 102 removed outlier: 6.782A pdb=" N THR F 101 " --> pdb=" O TYR I 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'H' and resid 83 through 84 removed outlier: 7.563A pdb=" N ARG H 83 " --> pdb=" O VAL I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'J' and resid 42 through 43 removed outlier: 7.602A pdb=" N ARG J 42 " --> pdb=" O ILE K 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'J' and resid 77 through 78 removed outlier: 3.616A pdb=" N ILE J 78 " --> pdb=" O GLY K 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 517 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 766 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3729 1.33 - 1.45: 4551 1.45 - 1.57: 7896 1.57 - 1.69: 620 1.69 - 1.81: 80 Bond restraints: 16876 Sorted by residual: bond pdb=" C1' DC U -58 " pdb=" N1 DC U -58 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C1' DC T 7 " pdb=" N1 DC T 7 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.33e+01 bond pdb=" C1' DT U 15 " pdb=" N1 DT U 15 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C1' DC T 6 " pdb=" N1 DC T 6 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.20e+01 bond pdb=" C3' DA U -38 " pdb=" C2' DA U -38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 ... (remaining 16871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 23158 2.01 - 4.01: 924 4.01 - 6.02: 27 6.02 - 8.03: 6 8.03 - 10.04: 4 Bond angle restraints: 24119 Sorted by residual: angle pdb=" O4' DT U 67 " pdb=" C1' DT U 67 " pdb=" N1 DT U 67 " ideal model delta sigma weight residual 108.00 112.17 -4.17 7.00e-01 2.04e+00 3.55e+01 angle pdb=" O4' DC T 7 " pdb=" C4' DC T 7 " pdb=" C3' DC T 7 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DT U -46 " pdb=" C1' DT U -46 " pdb=" N1 DT U -46 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" O4' DG T -68 " pdb=" C1' DG T -68 " pdb=" N9 DG T -68 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" O4' DC U 52 " pdb=" C4' DC U 52 " pdb=" C3' DC U 52 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.15e+01 ... (remaining 24114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 6869 18.23 - 36.46: 1167 36.46 - 54.69: 1069 54.69 - 72.91: 240 72.91 - 91.14: 12 Dihedral angle restraints: 9357 sinusoidal: 5864 harmonic: 3493 Sorted by residual: dihedral pdb=" CA PHE C 603 " pdb=" C PHE C 603 " pdb=" N SER C 604 " pdb=" CA SER C 604 " ideal model delta harmonic sigma weight residual 180.00 159.22 20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN C 562 " pdb=" C ASN C 562 " pdb=" N ARG C 563 " pdb=" CA ARG C 563 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ILE C 627 " pdb=" C ILE C 627 " pdb=" N ALA C 628 " pdb=" CA ALA C 628 " ideal model delta harmonic sigma weight residual -180.00 -164.11 -15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 9354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2040 0.047 - 0.095: 324 0.095 - 0.142: 293 0.142 - 0.189: 47 0.189 - 0.237: 2 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA VAL C 606 " pdb=" N VAL C 606 " pdb=" C VAL C 606 " pdb=" CB VAL C 606 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 745 " pdb=" N ARG A 745 " pdb=" C ARG A 745 " pdb=" CB ARG A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" C3' SAH A1008 " pdb=" C2' SAH A1008 " pdb=" C4' SAH A1008 " pdb=" O3' SAH A1008 " both_signs ideal model delta sigma weight residual False -2.71 -2.52 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2703 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U -27 " -0.032 2.00e-02 2.50e+03 2.96e-02 1.97e+01 pdb=" N1 DC U -27 " 0.072 2.00e-02 2.50e+03 pdb=" C2 DC U -27 " -0.038 2.00e-02 2.50e+03 pdb=" O2 DC U -27 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC U -27 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC U -27 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC U -27 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DC U -27 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC U -27 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC U 41 " 0.028 2.00e-02 2.50e+03 2.82e-02 1.79e+01 pdb=" N1 DC U 41 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DC U 41 " 0.041 2.00e-02 2.50e+03 pdb=" O2 DC U 41 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC U 41 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC U 41 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC U 41 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC U 41 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT U 14 " 0.032 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" N1 DT U 14 " -0.070 2.00e-02 2.50e+03 pdb=" C2 DT U 14 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT U 14 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT U 14 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT U 14 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DT U 14 " 0.003 2.00e-02 2.50e+03 pdb=" C7 DT U 14 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT U 14 " 0.001 2.00e-02 2.50e+03 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 27 2.39 - 3.02: 8377 3.02 - 3.65: 26442 3.65 - 4.27: 38411 4.27 - 4.90: 57802 Nonbonded interactions: 131059 Sorted by model distance: nonbonded pdb=" O LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 1.763 3.120 nonbonded pdb=" OG1 THR G 29 " pdb=" OP1 DT T 30 " model vdw 2.036 3.040 nonbonded pdb=" C LYS A 615 " pdb=" NH1 ARG A 626 " model vdw 2.068 3.350 nonbonded pdb=" OD1 ASP C 675 " pdb=" N LYS C 676 " model vdw 2.123 3.120 nonbonded pdb=" OE2 GLU A 658 " pdb=" NE ARG A 725 " model vdw 2.209 3.120 ... (remaining 131054 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 'E' and resid 25 through 102) selection = chain 'I' } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 16 through 118) } ncs_group { reference = (chain 'G' and resid 29 through 121) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.990 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.006 0.066 16904 Z= 0.498 Angle : 0.785 10.036 24155 Z= 0.661 Chirality : 0.053 0.237 2706 Planarity : 0.004 0.030 1989 Dihedral : 24.584 91.143 7093 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.25 % Favored : 97.40 % Rotamer: Outliers : 0.40 % Allowed : 1.29 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.23), residues: 1155 helix: 0.52 (0.19), residues: 677 sheet: -2.90 (1.27), residues: 14 loop : -2.36 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 593 TYR 0.011 0.001 TYR K 37 PHE 0.006 0.001 PHE C 603 TRP 0.006 0.001 TRP C 617 HIS 0.008 0.001 HIS I 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.50 (16876) covalent geometry : angle 0.77235 / 0.66 (24119) hydrogen bonds : bond 0.10391 / 6.30 ( 900) hydrogen bonds : angle 4.21913 / 2.76 ( 2290) metal coordination : bond 0.00551 / 0.40 ( 28) metal coordination : angle 3.76391 / 2.78 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 0.402 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: A 696 THR cc_start: 0.6129 (m) cc_final: 0.5893 (p) REVERT: A 719 MET cc_start: 0.7885 (tpp) cc_final: 0.7678 (tpp) REVERT: C 632 MET cc_start: 0.8165 (mmp) cc_final: 0.7864 (mmp) REVERT: C 649 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8414 (mmtm) REVERT: D 45 THR cc_start: 0.7940 (m) cc_final: 0.7601 (m) REVERT: D 50 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8684 (pt0) REVERT: D 86 SER cc_start: 0.8499 (p) cc_final: 0.7937 (m) REVERT: D 90 MET cc_start: 0.8481 (mmt) cc_final: 0.8190 (mmp) REVERT: D 93 GLN cc_start: 0.9194 (tt0) cc_final: 0.8714 (tt0) REVERT: D 97 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8822 (mt-10) REVERT: D 99 TYR cc_start: 0.8382 (t80) cc_final: 0.7238 (t80) REVERT: D 103 LEU cc_start: 0.9100 (tp) cc_final: 0.8843 (tt) REVERT: D 107 THR cc_start: 0.9501 (m) cc_final: 0.9081 (m) REVERT: D 125 GLN cc_start: 0.9183 (mt0) cc_final: 0.8559 (mm110) REVERT: E 74 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8415 (tp30) REVERT: E 79 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8196 (mmtm) REVERT: F 61 GLU cc_start: 0.8943 (tp30) cc_final: 0.8499 (tp30) REVERT: F 85 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (mt) REVERT: F 90 ASP cc_start: 0.8123 (t0) cc_final: 0.7472 (t70) REVERT: F 95 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9056 (tmtt) REVERT: F 97 LEU cc_start: 0.9398 (mt) cc_final: 0.9047 (mp) REVERT: G 37 TYR cc_start: 0.8042 (m-80) cc_final: 0.7096 (m-80) REVERT: G 40 LYS cc_start: 0.9065 (mttt) cc_final: 0.8826 (mmtp) REVERT: G 64 ASN cc_start: 0.8973 (m-40) cc_final: 0.8575 (t0) REVERT: G 91 ILE cc_start: 0.9486 (mm) cc_final: 0.9163 (tt) REVERT: G 102 GLU cc_start: 0.7164 (tp30) cc_final: 0.6753 (tp30) REVERT: H 41 TYR cc_start: 0.7768 (m-80) cc_final: 0.7411 (m-80) REVERT: H 79 LYS cc_start: 0.7791 (tttm) cc_final: 0.7543 (mptt) REVERT: H 80 THR cc_start: 0.7915 (t) cc_final: 0.7154 (t) REVERT: H 120 MET cc_start: 0.7660 (mtt) cc_final: 0.7055 (mtt) REVERT: I 49 LEU cc_start: 0.9027 (mt) cc_final: 0.8389 (mm) REVERT: I 55 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8609 (mtm180) REVERT: I 68 ASP cc_start: 0.8528 (m-30) cc_final: 0.8294 (m-30) REVERT: J 39 TYR cc_start: 0.8113 (m-80) cc_final: 0.7380 (m-80) REVERT: J 56 GLU cc_start: 0.8599 (tt0) cc_final: 0.8375 (tt0) REVERT: J 68 ASN cc_start: 0.7348 (m-40) cc_final: 0.6958 (m-40) REVERT: J 89 ASN cc_start: 0.8737 (m-40) cc_final: 0.8401 (t0) REVERT: J 92 GLU cc_start: 0.7144 (mt-10) cc_final: 0.5803 (mt-10) REVERT: J 94 ASN cc_start: 0.8746 (t0) cc_final: 0.7875 (m-40) REVERT: J 95 LYS cc_start: 0.8987 (tttt) cc_final: 0.8634 (ttpt) REVERT: K 92 GLN cc_start: 0.8800 (tt0) cc_final: 0.8328 (tm-30) outliers start: 4 outliers final: 1 residues processed: 453 average time/residue: 0.1400 time to fit residues: 87.5048 Evaluate side-chains 241 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 624 HIS D 68 GLN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN H 68 GLN H 125 GLN K 79 HIS ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.072518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.058299 restraints weight = 91552.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059727 restraints weight = 51873.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060688 restraints weight = 35285.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061303 restraints weight = 27219.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061694 restraints weight = 22999.225| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.180 16904 Z= 0.171 Angle : 0.716 36.206 24155 Z= 0.386 Chirality : 0.043 0.198 2706 Planarity : 0.005 0.046 1989 Dihedral : 28.837 89.276 4740 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % Rotamer: Outliers : 0.30 % Allowed : 3.07 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1155 helix: 1.02 (0.19), residues: 689 sheet: -1.75 (1.50), residues: 10 loop : -1.86 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 593 TYR 0.029 0.002 TYR F 39 PHE 0.014 0.002 PHE A 456 TRP 0.021 0.002 TRP C 591 HIS 0.014 0.002 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (16876) covalent geometry : angle 0.65110 / 0.38 (24119) hydrogen bonds : bond 0.05173 / 3.33 ( 900) hydrogen bonds : angle 3.63209 / 2.45 ( 2290) metal coordination : bond 0.03501 / 1.76 ( 28) metal coordination : angle 7.72916 / 4.63 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 0.277 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: A 687 LEU cc_start: 0.8983 (tp) cc_final: 0.8483 (tp) REVERT: A 696 THR cc_start: 0.7147 (m) cc_final: 0.6931 (p) REVERT: A 719 MET cc_start: 0.7676 (tpp) cc_final: 0.7412 (tpp) REVERT: C 594 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7324 (tp30) REVERT: C 598 THR cc_start: 0.7798 (t) cc_final: 0.7562 (p) REVERT: C 603 PHE cc_start: 0.6793 (m-80) cc_final: 0.6035 (m-10) REVERT: C 630 ASN cc_start: 0.6696 (p0) cc_final: 0.5787 (p0) REVERT: C 637 MET cc_start: 0.8580 (mmt) cc_final: 0.8062 (ppp) REVERT: C 657 MET cc_start: 0.4879 (tpp) cc_final: 0.4561 (mmp) REVERT: D 54 TYR cc_start: 0.8465 (m-10) cc_final: 0.8214 (m-10) REVERT: D 86 SER cc_start: 0.8930 (p) cc_final: 0.7945 (m) REVERT: D 90 MET cc_start: 0.8626 (mmt) cc_final: 0.8313 (mmm) REVERT: D 97 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8375 (mt-10) REVERT: D 99 TYR cc_start: 0.8734 (t80) cc_final: 0.7614 (t80) REVERT: D 107 THR cc_start: 0.9457 (m) cc_final: 0.9246 (m) REVERT: D 110 CYS cc_start: 0.8173 (t) cc_final: 0.7964 (t) REVERT: E 63 GLU cc_start: 0.8698 (tp30) cc_final: 0.8452 (tp30) REVERT: E 74 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8457 (tp30) REVERT: E 79 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8029 (mmtm) REVERT: E 88 TYR cc_start: 0.8407 (m-10) cc_final: 0.7414 (m-10) REVERT: F 29 ARG cc_start: 0.6934 (mtp85) cc_final: 0.5287 (ttm170) REVERT: F 38 ASN cc_start: 0.7778 (t0) cc_final: 0.7261 (t0) REVERT: F 61 GLU cc_start: 0.9093 (tp30) cc_final: 0.8553 (tp30) REVERT: F 90 ASP cc_start: 0.8384 (t0) cc_final: 0.7791 (t70) REVERT: G 40 LYS cc_start: 0.9321 (mttt) cc_final: 0.9013 (mmtp) REVERT: G 64 ASN cc_start: 0.8947 (m-40) cc_final: 0.8485 (t0) REVERT: G 81 ASN cc_start: 0.8876 (t0) cc_final: 0.8603 (t0) REVERT: H 46 VAL cc_start: 0.9403 (t) cc_final: 0.8929 (t) REVERT: H 82 LEU cc_start: 0.8011 (tp) cc_final: 0.7006 (tp) REVERT: H 120 MET cc_start: 0.7953 (mtt) cc_final: 0.7055 (mmm) REVERT: I 63 GLU cc_start: 0.8349 (tp30) cc_final: 0.8033 (tm-30) REVERT: J 56 GLU cc_start: 0.8685 (tt0) cc_final: 0.8317 (tt0) REVERT: J 64 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7683 (tp30) REVERT: J 68 ASN cc_start: 0.8352 (m-40) cc_final: 0.7863 (m-40) REVERT: J 82 HIS cc_start: 0.8857 (m170) cc_final: 0.8500 (m90) REVERT: J 87 VAL cc_start: 0.9462 (m) cc_final: 0.9250 (m) REVERT: J 89 ASN cc_start: 0.8712 (m-40) cc_final: 0.8350 (t0) REVERT: J 94 ASN cc_start: 0.8792 (t0) cc_final: 0.7661 (m-40) REVERT: J 95 LYS cc_start: 0.8965 (tttt) cc_final: 0.8579 (ttpt) REVERT: K 70 ILE cc_start: 0.9536 (mm) cc_final: 0.9268 (mm) REVERT: K 90 GLU cc_start: 0.9558 (mp0) cc_final: 0.8929 (mp0) REVERT: K 92 GLN cc_start: 0.9177 (tt0) cc_final: 0.8321 (tm-30) outliers start: 3 outliers final: 0 residues processed: 294 average time/residue: 0.1158 time to fit residues: 49.6109 Evaluate side-chains 226 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 144 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 113 optimal weight: 0.0020 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 624 HIS F 38 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.071635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.057473 restraints weight = 93612.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.058918 restraints weight = 52667.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059886 restraints weight = 35561.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060529 restraints weight = 27337.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060874 restraints weight = 22996.572| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.293 16904 Z= 0.165 Angle : 0.677 33.202 24155 Z= 0.367 Chirality : 0.041 0.205 2706 Planarity : 0.005 0.113 1989 Dihedral : 29.156 89.758 4740 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.55 % Favored : 96.36 % Rotamer: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.25), residues: 1155 helix: 1.32 (0.20), residues: 695 sheet: -1.52 (1.50), residues: 10 loop : -1.61 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 67 TYR 0.011 0.001 TYR K 39 PHE 0.023 0.001 PHE F 25 TRP 0.022 0.002 TRP C 617 HIS 0.014 0.002 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (16876) covalent geometry : angle 0.61647 / 0.36 (24119) hydrogen bonds : bond 0.04741 / 3.04 ( 900) hydrogen bonds : angle 3.51795 / 2.41 ( 2290) metal coordination : bond 0.05597 / 2.81 ( 28) metal coordination : angle 7.30406 / 4.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9365 (pt0) cc_final: 0.9102 (mm-30) REVERT: A 687 LEU cc_start: 0.8979 (tp) cc_final: 0.8472 (tp) REVERT: A 696 THR cc_start: 0.7734 (m) cc_final: 0.7468 (p) REVERT: A 719 MET cc_start: 0.7665 (tpp) cc_final: 0.7463 (tpp) REVERT: C 594 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7219 (tp30) REVERT: C 598 THR cc_start: 0.8038 (t) cc_final: 0.7805 (p) REVERT: C 600 ILE cc_start: 0.6234 (tp) cc_final: 0.6031 (tp) REVERT: C 603 PHE cc_start: 0.5866 (m-80) cc_final: 0.5232 (m-80) REVERT: C 614 MET cc_start: 0.6176 (mtp) cc_final: 0.5917 (mtm) REVERT: C 630 ASN cc_start: 0.6334 (p0) cc_final: 0.5956 (p0) REVERT: C 637 MET cc_start: 0.8342 (mmt) cc_final: 0.8081 (ppp) REVERT: C 657 MET cc_start: 0.4613 (tpp) cc_final: 0.4381 (mmm) REVERT: C 663 MET cc_start: 0.4996 (mtm) cc_final: 0.4374 (mtp) REVERT: D 61 LEU cc_start: 0.9239 (mp) cc_final: 0.8871 (mp) REVERT: D 86 SER cc_start: 0.8864 (p) cc_final: 0.8527 (p) REVERT: D 93 GLN cc_start: 0.9439 (tt0) cc_final: 0.8931 (tm-30) REVERT: D 97 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8638 (mt-10) REVERT: D 110 CYS cc_start: 0.8193 (t) cc_final: 0.7879 (t) REVERT: E 49 LEU cc_start: 0.9135 (mt) cc_final: 0.8113 (mt) REVERT: E 53 GLU cc_start: 0.8677 (mp0) cc_final: 0.8277 (mp0) REVERT: E 63 GLU cc_start: 0.8679 (tp30) cc_final: 0.8474 (tp30) REVERT: E 74 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8463 (tp30) REVERT: E 79 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8066 (mmtm) REVERT: E 88 TYR cc_start: 0.8377 (m-10) cc_final: 0.7327 (m-10) REVERT: F 56 GLU cc_start: 0.9420 (tt0) cc_final: 0.8973 (mt-10) REVERT: F 57 TYR cc_start: 0.8996 (t80) cc_final: 0.8507 (t80) REVERT: F 61 GLU cc_start: 0.9109 (tp30) cc_final: 0.8614 (tp30) REVERT: F 90 ASP cc_start: 0.8540 (t0) cc_final: 0.8014 (t70) REVERT: G 37 TYR cc_start: 0.7890 (m-80) cc_final: 0.7112 (m-80) REVERT: G 40 LYS cc_start: 0.9335 (mttt) cc_final: 0.8999 (mmtp) REVERT: G 64 ASN cc_start: 0.9003 (m-40) cc_final: 0.8530 (t0) REVERT: G 81 ASN cc_start: 0.8899 (t0) cc_final: 0.8568 (t0) REVERT: G 102 GLU cc_start: 0.7887 (tp30) cc_final: 0.7649 (tp30) REVERT: H 46 VAL cc_start: 0.9364 (t) cc_final: 0.8960 (t) REVERT: H 82 LEU cc_start: 0.8281 (tp) cc_final: 0.7810 (tp) REVERT: H 120 MET cc_start: 0.7808 (mtt) cc_final: 0.6894 (mmm) REVERT: I 43 VAL cc_start: 0.9365 (t) cc_final: 0.9052 (p) REVERT: J 56 GLU cc_start: 0.8532 (tt0) cc_final: 0.8186 (mt-10) REVERT: J 64 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7637 (tp30) REVERT: J 68 ASN cc_start: 0.7802 (m-40) cc_final: 0.7137 (m-40) REVERT: J 82 HIS cc_start: 0.8827 (m170) cc_final: 0.8318 (m-70) REVERT: J 89 ASN cc_start: 0.8702 (m-40) cc_final: 0.8491 (t0) REVERT: J 94 ASN cc_start: 0.8633 (t0) cc_final: 0.7408 (m-40) REVERT: J 95 LYS cc_start: 0.8969 (tttt) cc_final: 0.8611 (ttpt) REVERT: K 70 ILE cc_start: 0.9584 (mm) cc_final: 0.9345 (mm) REVERT: K 90 GLU cc_start: 0.9505 (mp0) cc_final: 0.8888 (mp0) REVERT: K 92 GLN cc_start: 0.9151 (tt0) cc_final: 0.8471 (tm-30) REVERT: K 96 ARG cc_start: 0.8479 (mtt180) cc_final: 0.8185 (tpp80) REVERT: K 99 LEU cc_start: 0.8426 (mt) cc_final: 0.8029 (mp) REVERT: K 103 LEU cc_start: 0.9184 (tp) cc_final: 0.8655 (mm) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.1144 time to fit residues: 47.5675 Evaluate side-chains 218 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 132 optimal weight: 9.9990 chunk 89 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.067759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.053714 restraints weight = 91097.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055036 restraints weight = 52372.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055915 restraints weight = 35956.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056461 restraints weight = 27945.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.056860 restraints weight = 23788.972| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 16904 Z= 0.226 Angle : 0.750 29.401 24155 Z= 0.399 Chirality : 0.044 0.209 2706 Planarity : 0.005 0.062 1989 Dihedral : 29.559 89.142 4740 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1155 helix: 1.25 (0.19), residues: 688 sheet: -1.03 (1.69), residues: 10 loop : -1.59 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 29 TYR 0.021 0.002 TYR A 754 PHE 0.018 0.002 PHE A 295 TRP 0.008 0.002 TRP C 617 HIS 0.006 0.002 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.22 (16876) covalent geometry : angle 0.70757 / 0.40 (24119) hydrogen bonds : bond 0.05823 / 3.74 ( 900) hydrogen bonds : angle 3.78449 / 2.58 ( 2290) metal coordination : bond 0.05264 / 2.65 ( 28) metal coordination : angle 6.46602 / 3.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 473 GLU cc_start: 0.9411 (pt0) cc_final: 0.9147 (mm-30) REVERT: A 687 LEU cc_start: 0.9014 (tp) cc_final: 0.8554 (tp) REVERT: A 696 THR cc_start: 0.7728 (m) cc_final: 0.7472 (p) REVERT: A 719 MET cc_start: 0.7756 (tpp) cc_final: 0.7519 (tpt) REVERT: C 603 PHE cc_start: 0.6112 (m-80) cc_final: 0.5391 (m-80) REVERT: C 614 MET cc_start: 0.6376 (mtp) cc_final: 0.6154 (mtm) REVERT: C 637 MET cc_start: 0.8287 (mmt) cc_final: 0.7999 (ppp) REVERT: C 646 LYS cc_start: 0.9312 (mmpt) cc_final: 0.8910 (tptp) REVERT: C 657 MET cc_start: 0.5743 (tpp) cc_final: 0.5446 (tpp) REVERT: C 663 MET cc_start: 0.5119 (mtm) cc_final: 0.4746 (mtm) REVERT: D 86 SER cc_start: 0.9218 (p) cc_final: 0.8923 (p) REVERT: D 90 MET cc_start: 0.8649 (mmp) cc_final: 0.8274 (mmm) REVERT: D 97 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8545 (mt-10) REVERT: D 120 MET cc_start: 0.8489 (mmm) cc_final: 0.8070 (mmm) REVERT: E 70 VAL cc_start: 0.9706 (t) cc_final: 0.8981 (m) REVERT: E 74 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8819 (mt-10) REVERT: E 88 TYR cc_start: 0.8504 (m-10) cc_final: 0.7710 (m-10) REVERT: F 56 GLU cc_start: 0.9397 (tt0) cc_final: 0.9169 (tt0) REVERT: F 61 GLU cc_start: 0.9146 (tp30) cc_final: 0.8660 (tp30) REVERT: F 90 ASP cc_start: 0.8441 (t0) cc_final: 0.7699 (t70) REVERT: G 29 THR cc_start: 0.7820 (p) cc_final: 0.7616 (p) REVERT: G 40 LYS cc_start: 0.9330 (mttt) cc_final: 0.8996 (mmtp) REVERT: G 51 ILE cc_start: 0.8907 (tt) cc_final: 0.8491 (tt) REVERT: G 56 MET cc_start: 0.8796 (tpp) cc_final: 0.8479 (tpp) REVERT: G 64 ASN cc_start: 0.9114 (m-40) cc_final: 0.8752 (t0) REVERT: G 81 ASN cc_start: 0.8929 (t0) cc_final: 0.8632 (t0) REVERT: H 46 VAL cc_start: 0.9245 (t) cc_final: 0.8858 (t) REVERT: H 80 THR cc_start: 0.8290 (p) cc_final: 0.8012 (p) REVERT: H 120 MET cc_start: 0.7991 (mtt) cc_final: 0.7516 (mmm) REVERT: H 123 ASP cc_start: 0.8868 (m-30) cc_final: 0.8494 (m-30) REVERT: H 124 ILE cc_start: 0.8902 (tt) cc_final: 0.8598 (tt) REVERT: I 43 VAL cc_start: 0.9480 (t) cc_final: 0.9175 (p) REVERT: I 53 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8925 (tm-30) REVERT: I 63 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8431 (mt-10) REVERT: I 64 ASN cc_start: 0.7965 (m-40) cc_final: 0.7649 (m-40) REVERT: J 56 GLU cc_start: 0.8647 (tt0) cc_final: 0.8358 (tt0) REVERT: J 64 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8414 (tp30) REVERT: J 68 ASN cc_start: 0.7926 (m-40) cc_final: 0.7711 (m-40) REVERT: J 89 ASN cc_start: 0.8846 (m-40) cc_final: 0.8627 (t0) REVERT: J 94 ASN cc_start: 0.8568 (t0) cc_final: 0.8248 (t0) REVERT: J 95 LYS cc_start: 0.9139 (tttt) cc_final: 0.8802 (ttpt) REVERT: K 90 GLU cc_start: 0.9469 (mp0) cc_final: 0.8946 (mp0) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1194 time to fit residues: 46.0779 Evaluate side-chains 207 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 5.9990 chunk 107 optimal weight: 0.0010 chunk 133 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 631 GLN H 85 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.068449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054284 restraints weight = 90660.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055728 restraints weight = 50374.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.056691 restraints weight = 33737.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.057254 restraints weight = 25737.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057706 restraints weight = 21758.536| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 16904 Z= 0.161 Angle : 0.669 34.865 24155 Z= 0.360 Chirality : 0.041 0.209 2706 Planarity : 0.004 0.049 1989 Dihedral : 29.581 89.429 4740 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1155 helix: 1.49 (0.20), residues: 689 sheet: -0.95 (1.69), residues: 10 loop : -1.49 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 92 TYR 0.025 0.001 TYR E 98 PHE 0.014 0.001 PHE A 456 TRP 0.009 0.001 TRP C 617 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (16876) covalent geometry : angle 0.60653 / 0.35 (24119) hydrogen bonds : bond 0.04634 / 3.00 ( 900) hydrogen bonds : angle 3.57758 / 2.48 ( 2290) metal coordination : bond 0.04985 / 2.50 ( 28) metal coordination : angle 7.33797 / 4.52 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.2606 (ptm) cc_final: 0.1818 (tmm) REVERT: A 473 GLU cc_start: 0.9451 (pt0) cc_final: 0.9205 (mm-30) REVERT: A 687 LEU cc_start: 0.9038 (tp) cc_final: 0.8576 (tp) REVERT: A 696 THR cc_start: 0.7927 (m) cc_final: 0.7668 (p) REVERT: C 603 PHE cc_start: 0.5594 (m-80) cc_final: 0.4890 (m-80) REVERT: C 637 MET cc_start: 0.8284 (mmt) cc_final: 0.8016 (ppp) REVERT: C 646 LYS cc_start: 0.9345 (mmpt) cc_final: 0.8881 (ttmt) REVERT: C 657 MET cc_start: 0.5907 (tpp) cc_final: 0.5685 (tpp) REVERT: C 663 MET cc_start: 0.5599 (mtm) cc_final: 0.5199 (mtm) REVERT: D 50 GLU cc_start: 0.8817 (tp30) cc_final: 0.8616 (tp30) REVERT: D 86 SER cc_start: 0.9117 (p) cc_final: 0.8856 (p) REVERT: D 90 MET cc_start: 0.8791 (mmp) cc_final: 0.8435 (mmm) REVERT: D 97 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8147 (mt-10) REVERT: E 63 GLU cc_start: 0.8829 (tp30) cc_final: 0.8573 (tp30) REVERT: E 74 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8669 (tp30) REVERT: E 88 TYR cc_start: 0.8523 (m-10) cc_final: 0.7927 (m-10) REVERT: E 98 TYR cc_start: 0.8940 (m-80) cc_final: 0.8336 (m-10) REVERT: F 56 GLU cc_start: 0.9424 (tt0) cc_final: 0.9028 (mt-10) REVERT: F 61 GLU cc_start: 0.9100 (tp30) cc_final: 0.8539 (tp30) REVERT: F 90 ASP cc_start: 0.8604 (t0) cc_final: 0.7786 (t70) REVERT: G 40 LYS cc_start: 0.9336 (mttt) cc_final: 0.8988 (mmtp) REVERT: G 64 ASN cc_start: 0.9090 (m-40) cc_final: 0.8740 (t0) REVERT: G 105 LYS cc_start: 0.9134 (mppt) cc_final: 0.8821 (mmtp) REVERT: H 46 VAL cc_start: 0.9236 (t) cc_final: 0.8850 (t) REVERT: H 80 THR cc_start: 0.8190 (p) cc_final: 0.7944 (p) REVERT: H 107 THR cc_start: 0.9449 (m) cc_final: 0.9052 (p) REVERT: H 120 MET cc_start: 0.7929 (mtt) cc_final: 0.7514 (mmm) REVERT: H 123 ASP cc_start: 0.8766 (m-30) cc_final: 0.8565 (m-30) REVERT: H 124 ILE cc_start: 0.8853 (tt) cc_final: 0.8519 (tt) REVERT: I 37 LEU cc_start: 0.9347 (mt) cc_final: 0.9089 (mt) REVERT: I 43 VAL cc_start: 0.9485 (t) cc_final: 0.9109 (p) REVERT: I 64 ASN cc_start: 0.8157 (m-40) cc_final: 0.7788 (m-40) REVERT: I 68 ASP cc_start: 0.8232 (m-30) cc_final: 0.8003 (m-30) REVERT: J 36 LYS cc_start: 0.8899 (mmtp) cc_final: 0.8697 (mttp) REVERT: J 56 GLU cc_start: 0.8463 (tt0) cc_final: 0.8236 (tt0) REVERT: J 64 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8349 (tp30) REVERT: J 68 ASN cc_start: 0.7967 (m-40) cc_final: 0.7680 (m-40) REVERT: J 89 ASN cc_start: 0.8800 (m-40) cc_final: 0.8579 (t0) REVERT: J 94 ASN cc_start: 0.8626 (t0) cc_final: 0.8037 (m-40) REVERT: J 95 LYS cc_start: 0.9112 (tttt) cc_final: 0.8707 (tmmt) REVERT: J 99 ARG cc_start: 0.8028 (mpt180) cc_final: 0.7579 (mmt180) REVERT: K 49 THR cc_start: 0.7812 (m) cc_final: 0.7317 (p) REVERT: K 65 ASP cc_start: 0.8821 (t70) cc_final: 0.8570 (t0) REVERT: K 70 ILE cc_start: 0.9631 (mm) cc_final: 0.9405 (mm) REVERT: K 90 GLU cc_start: 0.9515 (mp0) cc_final: 0.9027 (mp0) REVERT: K 103 LEU cc_start: 0.8837 (tp) cc_final: 0.8573 (mm) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1274 time to fit residues: 48.0331 Evaluate side-chains 202 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 42 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 102 optimal weight: 0.2980 chunk 128 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN E 93 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053264 restraints weight = 92463.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054608 restraints weight = 53205.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055489 restraints weight = 36712.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.056097 restraints weight = 28676.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056476 restraints weight = 24390.149| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.229 16904 Z= 0.184 Angle : 0.676 25.275 24155 Z= 0.370 Chirality : 0.042 0.211 2706 Planarity : 0.005 0.089 1989 Dihedral : 29.681 88.855 4740 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1155 helix: 1.48 (0.20), residues: 688 sheet: -0.69 (1.68), residues: 10 loop : -1.44 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 63 TYR 0.024 0.001 TYR J 39 PHE 0.013 0.002 PHE C 626 TRP 0.010 0.001 TRP C 617 HIS 0.010 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (16876) covalent geometry : angle 0.63855 / 0.37 (24119) hydrogen bonds : bond 0.04885 / 3.14 ( 900) hydrogen bonds : angle 3.66036 / 2.55 ( 2290) metal coordination : bond 0.04362 / 2.19 ( 28) metal coordination : angle 5.81039 / 3.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.2110 (ptm) cc_final: 0.1342 (tmm) REVERT: A 473 GLU cc_start: 0.9478 (pt0) cc_final: 0.9224 (mm-30) REVERT: A 687 LEU cc_start: 0.8994 (tp) cc_final: 0.8526 (tp) REVERT: A 696 THR cc_start: 0.7929 (m) cc_final: 0.7678 (p) REVERT: C 603 PHE cc_start: 0.5728 (m-80) cc_final: 0.5126 (m-80) REVERT: C 614 MET cc_start: 0.6100 (mtm) cc_final: 0.5812 (mtp) REVERT: C 616 LEU cc_start: 0.8600 (mt) cc_final: 0.8399 (mt) REVERT: C 637 MET cc_start: 0.8265 (mmt) cc_final: 0.7971 (ppp) REVERT: C 646 LYS cc_start: 0.9255 (mmpt) cc_final: 0.8848 (tttm) REVERT: C 657 MET cc_start: 0.5870 (tpp) cc_final: 0.5601 (tpp) REVERT: D 86 SER cc_start: 0.9093 (p) cc_final: 0.8880 (p) REVERT: D 90 MET cc_start: 0.8674 (mmp) cc_final: 0.8349 (mmm) REVERT: D 97 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8461 (mt-10) REVERT: D 120 MET cc_start: 0.8236 (mmm) cc_final: 0.7741 (mmm) REVERT: E 74 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8680 (tp30) REVERT: E 88 TYR cc_start: 0.8412 (m-10) cc_final: 0.7809 (m-10) REVERT: E 98 TYR cc_start: 0.8869 (m-10) cc_final: 0.8384 (m-10) REVERT: F 61 GLU cc_start: 0.9085 (tp30) cc_final: 0.8560 (tp30) REVERT: F 90 ASP cc_start: 0.8751 (t0) cc_final: 0.8260 (t70) REVERT: G 40 LYS cc_start: 0.9328 (mttt) cc_final: 0.9004 (mmtp) REVERT: G 64 ASN cc_start: 0.9131 (m-40) cc_final: 0.8745 (t0) REVERT: H 46 VAL cc_start: 0.9299 (t) cc_final: 0.8916 (t) REVERT: H 80 THR cc_start: 0.8244 (p) cc_final: 0.7953 (p) REVERT: H 107 THR cc_start: 0.9420 (m) cc_final: 0.9028 (p) REVERT: H 120 MET cc_start: 0.8074 (mtt) cc_final: 0.7544 (mmm) REVERT: H 123 ASP cc_start: 0.8983 (m-30) cc_final: 0.8718 (m-30) REVERT: I 37 LEU cc_start: 0.9361 (mt) cc_final: 0.9096 (mt) REVERT: I 64 ASN cc_start: 0.8376 (m-40) cc_final: 0.7956 (m-40) REVERT: J 56 GLU cc_start: 0.8501 (tt0) cc_final: 0.8234 (tt0) REVERT: J 64 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8428 (tm-30) REVERT: J 68 ASN cc_start: 0.8139 (m-40) cc_final: 0.7756 (m-40) REVERT: J 89 ASN cc_start: 0.8783 (m-40) cc_final: 0.8543 (t0) REVERT: J 94 ASN cc_start: 0.8612 (t0) cc_final: 0.8227 (t0) REVERT: J 95 LYS cc_start: 0.9233 (tttt) cc_final: 0.8811 (ttpt) REVERT: J 99 ARG cc_start: 0.7985 (mpt180) cc_final: 0.7581 (mmt180) REVERT: K 49 THR cc_start: 0.7829 (m) cc_final: 0.7276 (p) REVERT: K 90 GLU cc_start: 0.9464 (mp0) cc_final: 0.8971 (mp0) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1286 time to fit residues: 48.5595 Evaluate side-chains 194 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 42 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.067924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.053759 restraints weight = 91805.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.055050 restraints weight = 53422.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.055918 restraints weight = 37054.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056509 restraints weight = 29022.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.056844 restraints weight = 24772.652| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.180 16904 Z= 0.155 Angle : 0.652 24.011 24155 Z= 0.359 Chirality : 0.041 0.207 2706 Planarity : 0.004 0.053 1989 Dihedral : 29.695 89.771 4740 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1155 helix: 1.53 (0.20), residues: 688 sheet: -1.78 (1.58), residues: 12 loop : -1.35 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 92 TYR 0.018 0.001 TYR D 99 PHE 0.028 0.002 PHE H 104 TRP 0.010 0.001 TRP C 617 HIS 0.008 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (16876) covalent geometry : angle 0.61459 / 0.36 (24119) hydrogen bonds : bond 0.04508 / 2.91 ( 900) hydrogen bonds : angle 3.61999 / 2.51 ( 2290) metal coordination : bond 0.03452 / 1.74 ( 28) metal coordination : angle 5.68083 / 3.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.7891 (tmm) cc_final: 0.7675 (tmm) REVERT: A 444 MET cc_start: 0.2019 (ptm) cc_final: 0.1123 (tmm) REVERT: A 473 GLU cc_start: 0.9475 (pt0) cc_final: 0.9217 (mm-30) REVERT: A 687 LEU cc_start: 0.8995 (tp) cc_final: 0.8410 (tp) REVERT: A 696 THR cc_start: 0.7904 (m) cc_final: 0.7651 (p) REVERT: C 603 PHE cc_start: 0.5656 (m-80) cc_final: 0.5137 (m-80) REVERT: C 614 MET cc_start: 0.6064 (mtm) cc_final: 0.5748 (mtp) REVERT: C 637 MET cc_start: 0.8378 (mmt) cc_final: 0.8123 (ppp) REVERT: C 646 LYS cc_start: 0.9213 (mmpt) cc_final: 0.8801 (tttm) REVERT: D 120 MET cc_start: 0.8529 (mmm) cc_final: 0.7977 (mmm) REVERT: E 63 GLU cc_start: 0.8655 (tp30) cc_final: 0.8243 (tp30) REVERT: E 74 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8644 (tp30) REVERT: E 88 TYR cc_start: 0.8388 (m-10) cc_final: 0.7766 (m-10) REVERT: E 98 TYR cc_start: 0.8739 (m-10) cc_final: 0.8370 (m-10) REVERT: F 61 GLU cc_start: 0.9052 (tp30) cc_final: 0.8518 (tp30) REVERT: F 90 ASP cc_start: 0.8794 (t0) cc_final: 0.8194 (t70) REVERT: F 97 LEU cc_start: 0.9265 (mp) cc_final: 0.9046 (mp) REVERT: G 29 THR cc_start: 0.7781 (p) cc_final: 0.7553 (p) REVERT: G 40 LYS cc_start: 0.9308 (mttt) cc_final: 0.9011 (mmtp) REVERT: G 64 ASN cc_start: 0.9090 (m-40) cc_final: 0.8754 (t0) REVERT: H 46 VAL cc_start: 0.9284 (t) cc_final: 0.8882 (t) REVERT: H 80 THR cc_start: 0.8198 (p) cc_final: 0.7912 (t) REVERT: H 81 ASP cc_start: 0.8107 (m-30) cc_final: 0.7904 (m-30) REVERT: H 90 MET cc_start: 0.8693 (mmp) cc_final: 0.8437 (ptp) REVERT: H 107 THR cc_start: 0.9407 (m) cc_final: 0.8966 (p) REVERT: H 120 MET cc_start: 0.8081 (mtt) cc_final: 0.7538 (mmm) REVERT: H 123 ASP cc_start: 0.8927 (m-30) cc_final: 0.8624 (m-30) REVERT: H 124 ILE cc_start: 0.8972 (tt) cc_final: 0.8668 (tt) REVERT: I 43 VAL cc_start: 0.9440 (t) cc_final: 0.9162 (p) REVERT: I 64 ASN cc_start: 0.8421 (m-40) cc_final: 0.7956 (m-40) REVERT: I 68 ASP cc_start: 0.8371 (m-30) cc_final: 0.7941 (m-30) REVERT: J 56 GLU cc_start: 0.8459 (tt0) cc_final: 0.8232 (tt0) REVERT: J 64 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8474 (tm-30) REVERT: J 68 ASN cc_start: 0.8196 (m-40) cc_final: 0.7795 (m-40) REVERT: J 90 ASP cc_start: 0.8702 (t70) cc_final: 0.8403 (t70) REVERT: J 94 ASN cc_start: 0.8597 (t0) cc_final: 0.8116 (m-40) REVERT: J 95 LYS cc_start: 0.9230 (tttt) cc_final: 0.8804 (tmmt) REVERT: J 99 ARG cc_start: 0.8030 (mpt180) cc_final: 0.7547 (mmt180) REVERT: K 49 THR cc_start: 0.7718 (m) cc_final: 0.7233 (p) REVERT: K 90 GLU cc_start: 0.9484 (mp0) cc_final: 0.9111 (mp0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1318 time to fit residues: 48.9539 Evaluate side-chains 204 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 71 optimal weight: 0.0050 chunk 122 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052798 restraints weight = 93070.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054099 restraints weight = 53562.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054980 restraints weight = 36954.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055555 restraints weight = 28907.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.055899 restraints weight = 24636.532| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 16904 Z= 0.182 Angle : 0.692 27.021 24155 Z= 0.376 Chirality : 0.041 0.198 2706 Planarity : 0.004 0.062 1989 Dihedral : 29.761 89.592 4740 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1155 helix: 1.44 (0.20), residues: 698 sheet: 0.01 (1.05), residues: 26 loop : -1.38 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 593 TYR 0.020 0.001 TYR D 99 PHE 0.022 0.001 PHE E 61 TRP 0.018 0.002 TRP C 617 HIS 0.011 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (16876) covalent geometry : angle 0.65251 / 0.37 (24119) hydrogen bonds : bond 0.04800 / 3.10 ( 900) hydrogen bonds : angle 3.70498 / 2.59 ( 2290) metal coordination : bond 0.04468 / 2.25 ( 28) metal coordination : angle 6.01272 / 3.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8081 (tmm) cc_final: 0.7870 (tmm) REVERT: A 444 MET cc_start: 0.2020 (ptm) cc_final: 0.1124 (tmm) REVERT: A 473 GLU cc_start: 0.9480 (pt0) cc_final: 0.9213 (mm-30) REVERT: A 687 LEU cc_start: 0.9018 (tp) cc_final: 0.8454 (tp) REVERT: C 603 PHE cc_start: 0.5469 (m-80) cc_final: 0.5178 (m-80) REVERT: C 614 MET cc_start: 0.6692 (mtm) cc_final: 0.6322 (mtp) REVERT: C 637 MET cc_start: 0.8352 (mmt) cc_final: 0.8117 (ppp) REVERT: C 646 LYS cc_start: 0.9223 (mmpt) cc_final: 0.8794 (tttm) REVERT: D 120 MET cc_start: 0.8288 (mmm) cc_final: 0.8011 (mmm) REVERT: E 74 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8681 (tp30) REVERT: E 88 TYR cc_start: 0.8431 (m-10) cc_final: 0.7710 (m-10) REVERT: E 98 TYR cc_start: 0.8906 (m-10) cc_final: 0.8460 (m-10) REVERT: F 57 TYR cc_start: 0.8874 (t80) cc_final: 0.8479 (t80) REVERT: F 61 GLU cc_start: 0.9057 (tp30) cc_final: 0.8583 (tp30) REVERT: F 97 LEU cc_start: 0.9326 (mp) cc_final: 0.9091 (mp) REVERT: G 40 LYS cc_start: 0.9319 (mttt) cc_final: 0.9001 (mmtp) REVERT: G 64 ASN cc_start: 0.9139 (m-40) cc_final: 0.8776 (t0) REVERT: G 105 LYS cc_start: 0.9327 (mppt) cc_final: 0.9102 (mmtp) REVERT: H 46 VAL cc_start: 0.9292 (t) cc_final: 0.8919 (t) REVERT: H 80 THR cc_start: 0.8251 (p) cc_final: 0.7965 (t) REVERT: H 81 ASP cc_start: 0.8159 (m-30) cc_final: 0.7913 (m-30) REVERT: H 90 MET cc_start: 0.8769 (mmp) cc_final: 0.8455 (ptp) REVERT: H 107 THR cc_start: 0.9394 (m) cc_final: 0.8990 (p) REVERT: H 123 ASP cc_start: 0.8848 (m-30) cc_final: 0.8423 (m-30) REVERT: H 124 ILE cc_start: 0.9075 (tt) cc_final: 0.8757 (tt) REVERT: I 43 VAL cc_start: 0.9456 (t) cc_final: 0.9179 (p) REVERT: I 64 ASN cc_start: 0.8472 (m-40) cc_final: 0.7996 (m-40) REVERT: I 68 ASP cc_start: 0.8421 (m-30) cc_final: 0.8001 (m-30) REVERT: J 39 TYR cc_start: 0.8655 (m-80) cc_final: 0.8301 (m-80) REVERT: J 56 GLU cc_start: 0.8484 (tt0) cc_final: 0.8257 (tt0) REVERT: J 64 GLU cc_start: 0.9143 (tm-30) cc_final: 0.8605 (tm-30) REVERT: J 68 ASN cc_start: 0.8310 (m-40) cc_final: 0.7908 (m-40) REVERT: J 94 ASN cc_start: 0.8657 (t0) cc_final: 0.8041 (m-40) REVERT: J 95 LYS cc_start: 0.9293 (tttt) cc_final: 0.8833 (ttpt) REVERT: J 99 ARG cc_start: 0.8039 (mpt180) cc_final: 0.7608 (mmt180) REVERT: K 49 THR cc_start: 0.7755 (m) cc_final: 0.7206 (p) REVERT: K 90 GLU cc_start: 0.9468 (mp0) cc_final: 0.9188 (mp0) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1343 time to fit residues: 49.5387 Evaluate side-chains 202 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 70 optimal weight: 0.0070 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 128 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN E 93 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.067702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.053597 restraints weight = 91697.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054910 restraints weight = 52296.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055795 restraints weight = 35937.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056382 restraints weight = 28048.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.056715 restraints weight = 23895.757| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.304 16904 Z= 0.148 Angle : 0.685 37.608 24155 Z= 0.364 Chirality : 0.041 0.188 2706 Planarity : 0.004 0.053 1989 Dihedral : 29.731 89.622 4740 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1155 helix: 1.57 (0.20), residues: 688 sheet: -0.44 (1.64), residues: 10 loop : -1.28 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 81 TYR 0.019 0.001 TYR D 99 PHE 0.026 0.001 PHE H 104 TRP 0.016 0.002 TRP C 617 HIS 0.012 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (16876) covalent geometry : angle 0.61966 / 0.36 (24119) hydrogen bonds : bond 0.04279 / 2.76 ( 900) hydrogen bonds : angle 3.51913 / 2.44 ( 2290) metal coordination : bond 0.05785 / 2.90 ( 28) metal coordination : angle 7.61591 / 4.65 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8104 (tmm) cc_final: 0.7892 (tmm) REVERT: A 444 MET cc_start: 0.1927 (ptm) cc_final: 0.1027 (tmm) REVERT: A 473 GLU cc_start: 0.9470 (pt0) cc_final: 0.9196 (mm-30) REVERT: A 687 LEU cc_start: 0.9045 (tp) cc_final: 0.8560 (tp) REVERT: C 590 GLU cc_start: 0.6850 (tp30) cc_final: 0.5962 (tp30) REVERT: C 614 MET cc_start: 0.6606 (mtm) cc_final: 0.6273 (mtp) REVERT: C 637 MET cc_start: 0.8351 (mmt) cc_final: 0.8112 (ppp) REVERT: C 646 LYS cc_start: 0.9328 (mmpt) cc_final: 0.8874 (ttmt) REVERT: D 50 GLU cc_start: 0.8923 (tp30) cc_final: 0.8666 (tp30) REVERT: D 64 LYS cc_start: 0.9445 (mmtp) cc_final: 0.9241 (mttm) REVERT: D 94 GLU cc_start: 0.8728 (pm20) cc_final: 0.8491 (pm20) REVERT: D 133 GLU cc_start: 0.7928 (mp0) cc_final: 0.7249 (pm20) REVERT: E 63 GLU cc_start: 0.8482 (tp30) cc_final: 0.8264 (tp30) REVERT: E 74 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8624 (tp30) REVERT: E 88 TYR cc_start: 0.8369 (m-10) cc_final: 0.7766 (m-10) REVERT: E 98 TYR cc_start: 0.8770 (m-10) cc_final: 0.8158 (m-10) REVERT: F 56 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8587 (mm-30) REVERT: F 57 TYR cc_start: 0.8856 (t80) cc_final: 0.8463 (t80) REVERT: F 61 GLU cc_start: 0.9044 (tp30) cc_final: 0.8510 (tp30) REVERT: F 97 LEU cc_start: 0.9270 (mp) cc_final: 0.9048 (mp) REVERT: G 40 LYS cc_start: 0.9315 (mttt) cc_final: 0.8962 (mmtp) REVERT: G 56 MET cc_start: 0.8686 (tpp) cc_final: 0.8357 (tpp) REVERT: G 64 ASN cc_start: 0.9107 (m-40) cc_final: 0.8754 (t0) REVERT: G 105 LYS cc_start: 0.9302 (mppt) cc_final: 0.9096 (mmtp) REVERT: H 46 VAL cc_start: 0.9251 (t) cc_final: 0.8844 (t) REVERT: H 80 THR cc_start: 0.8233 (p) cc_final: 0.7958 (t) REVERT: H 81 ASP cc_start: 0.8210 (m-30) cc_final: 0.7963 (m-30) REVERT: H 107 THR cc_start: 0.9375 (m) cc_final: 0.8937 (p) REVERT: H 123 ASP cc_start: 0.8728 (m-30) cc_final: 0.8391 (m-30) REVERT: H 124 ILE cc_start: 0.9035 (tt) cc_final: 0.8733 (tt) REVERT: I 39 ARG cc_start: 0.8912 (mpt180) cc_final: 0.8686 (mpt180) REVERT: I 43 VAL cc_start: 0.9447 (t) cc_final: 0.9100 (p) REVERT: I 64 ASN cc_start: 0.8339 (m-40) cc_final: 0.7931 (m-40) REVERT: I 68 ASP cc_start: 0.8422 (m-30) cc_final: 0.7956 (m-30) REVERT: J 39 TYR cc_start: 0.8634 (m-80) cc_final: 0.8343 (m-80) REVERT: J 56 GLU cc_start: 0.8457 (tt0) cc_final: 0.8190 (tt0) REVERT: J 64 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8638 (tm-30) REVERT: J 68 ASN cc_start: 0.8334 (m-40) cc_final: 0.7936 (m-40) REVERT: J 94 ASN cc_start: 0.8661 (t0) cc_final: 0.8144 (m-40) REVERT: J 95 LYS cc_start: 0.9239 (tttt) cc_final: 0.8736 (ttpt) REVERT: J 99 ARG cc_start: 0.8047 (mpt180) cc_final: 0.7584 (mmt180) REVERT: K 49 THR cc_start: 0.7554 (m) cc_final: 0.7130 (p) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1284 time to fit residues: 48.8855 Evaluate side-chains 209 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 62 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.052981 restraints weight = 92386.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054279 restraints weight = 53512.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055149 restraints weight = 37085.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.055692 restraints weight = 29038.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056090 restraints weight = 24864.104| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.281 16904 Z= 0.166 Angle : 0.692 34.913 24155 Z= 0.369 Chirality : 0.041 0.178 2706 Planarity : 0.004 0.054 1989 Dihedral : 29.759 89.871 4740 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1155 helix: 1.50 (0.20), residues: 698 sheet: -0.44 (1.60), residues: 10 loop : -1.26 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 89 TYR 0.022 0.001 TYR D 99 PHE 0.025 0.001 PHE E 61 TRP 0.023 0.003 TRP C 591 HIS 0.009 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (16876) covalent geometry : angle 0.63576 / 0.36 (24119) hydrogen bonds : bond 0.04477 / 2.89 ( 900) hydrogen bonds : angle 3.58989 / 2.49 ( 2290) metal coordination : bond 0.05340 / 2.68 ( 28) metal coordination : angle 7.07601 / 4.33 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8204 (tmm) cc_final: 0.8002 (tmm) REVERT: A 444 MET cc_start: 0.1950 (ptm) cc_final: 0.1034 (tmm) REVERT: A 473 GLU cc_start: 0.9455 (pt0) cc_final: 0.9170 (mm-30) REVERT: A 687 LEU cc_start: 0.8989 (tp) cc_final: 0.8404 (tp) REVERT: C 603 PHE cc_start: 0.5748 (m-80) cc_final: 0.5483 (m-80) REVERT: C 614 MET cc_start: 0.6708 (mtm) cc_final: 0.6371 (mtp) REVERT: C 646 LYS cc_start: 0.9206 (mmpt) cc_final: 0.8764 (ttmt) REVERT: D 50 GLU cc_start: 0.8929 (tp30) cc_final: 0.8669 (tp30) REVERT: D 64 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9204 (mttm) REVERT: D 90 MET cc_start: 0.8489 (mmp) cc_final: 0.8198 (mmp) REVERT: D 133 GLU cc_start: 0.7816 (mp0) cc_final: 0.7373 (mt-10) REVERT: E 74 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8646 (tp30) REVERT: E 88 TYR cc_start: 0.8413 (m-10) cc_final: 0.7685 (m-10) REVERT: E 98 TYR cc_start: 0.8915 (m-10) cc_final: 0.8400 (m-10) REVERT: F 56 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8602 (mm-30) REVERT: F 57 TYR cc_start: 0.8861 (t80) cc_final: 0.8462 (t80) REVERT: F 61 GLU cc_start: 0.9051 (tp30) cc_final: 0.8538 (tp30) REVERT: F 97 LEU cc_start: 0.9315 (mp) cc_final: 0.9111 (mp) REVERT: G 40 LYS cc_start: 0.9324 (mttt) cc_final: 0.8961 (mmtp) REVERT: G 56 MET cc_start: 0.8763 (tpp) cc_final: 0.8439 (tpp) REVERT: G 64 ASN cc_start: 0.9126 (m-40) cc_final: 0.8772 (t0) REVERT: H 46 VAL cc_start: 0.9268 (t) cc_final: 0.8886 (t) REVERT: H 80 THR cc_start: 0.8328 (p) cc_final: 0.8009 (t) REVERT: H 81 ASP cc_start: 0.8250 (m-30) cc_final: 0.7998 (m-30) REVERT: H 90 MET cc_start: 0.8955 (mmp) cc_final: 0.8647 (ptp) REVERT: H 107 THR cc_start: 0.9375 (m) cc_final: 0.8946 (t) REVERT: H 124 ILE cc_start: 0.9097 (tt) cc_final: 0.8737 (tt) REVERT: I 43 VAL cc_start: 0.9457 (t) cc_final: 0.9161 (p) REVERT: J 39 TYR cc_start: 0.8816 (m-80) cc_final: 0.8407 (m-80) REVERT: J 56 GLU cc_start: 0.8476 (tt0) cc_final: 0.8227 (tt0) REVERT: J 64 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8675 (tm-30) REVERT: J 68 ASN cc_start: 0.8393 (m-40) cc_final: 0.7950 (m-40) REVERT: J 94 ASN cc_start: 0.8678 (t0) cc_final: 0.8145 (m-40) REVERT: J 95 LYS cc_start: 0.9221 (tttt) cc_final: 0.8780 (tmmt) REVERT: J 99 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7638 (mmt180) REVERT: K 49 THR cc_start: 0.7373 (m) cc_final: 0.6989 (p) REVERT: K 92 GLN cc_start: 0.9164 (tt0) cc_final: 0.8213 (tm-30) REVERT: K 103 LEU cc_start: 0.8605 (mm) cc_final: 0.8337 (mm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1340 time to fit residues: 49.1553 Evaluate side-chains 205 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.066755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052656 restraints weight = 92131.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053951 restraints weight = 53516.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054823 restraints weight = 37107.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.055390 restraints weight = 29100.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055747 restraints weight = 24868.669| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 16904 Z= 0.163 Angle : 0.694 32.402 24155 Z= 0.372 Chirality : 0.041 0.193 2706 Planarity : 0.004 0.053 1989 Dihedral : 29.769 89.836 4740 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1155 helix: 1.50 (0.20), residues: 698 sheet: -0.51 (1.61), residues: 10 loop : -1.26 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 128 TYR 0.012 0.001 TYR J 39 PHE 0.012 0.001 PHE E 61 TRP 0.017 0.002 TRP C 591 HIS 0.009 0.001 HIS C 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (16876) covalent geometry : angle 0.64521 / 0.37 (24119) hydrogen bonds : bond 0.04452 / 2.87 ( 900) hydrogen bonds : angle 3.60342 / 2.51 ( 2290) metal coordination : bond 0.04436 / 2.23 ( 28) metal coordination : angle 6.68227 / 4.13 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2650.35 seconds wall clock time: 46 minutes 30.21 seconds (2790.21 seconds total)