Starting phenix.real_space_refine on Sun Jul 5 00:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3u_47496/07_2026/9e3u_47496.map" } resolution = 4.9 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= 0.010 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 9 6.06 5 P 330 5.49 5 S 116 5.16 5 C 13969 2.51 5 N 4349 2.21 5 O 4998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s 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: 23771 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 764 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "L" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3398 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3367 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "V" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2793 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 331} Chain breaks: 3 Chain: "Z" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1478 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Chain: "U" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "Y" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3404 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 22, 'TRANS': 401} Chain breaks: 1 Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' ZN': 3} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12794 SG CYS V 415 31.463 66.816 138.563 1.00999.99 S ATOM 12814 SG CYS V 418 35.095 67.616 137.169 1.00999.99 S ATOM 12944 SG CYS V 435 35.069 66.892 140.707 1.00999.99 S ATOM 12966 SG CYS V 438 33.731 69.825 139.744 1.00999.99 S ATOM 13148 SG CYS V 458 25.135 78.579 139.823 1.00999.99 S ATOM 13168 SG CYS V 461 27.662 76.788 137.037 1.00999.99 S ATOM 13310 SG CYS V 480 25.554 79.264 135.929 1.00999.99 S ATOM 13332 SG CYS V 483 24.528 76.014 136.544 1.00999.99 S ATOM 13237 SG CYS V 470 15.434 84.658 145.974 1.00999.99 S ATOM 13270 SG CYS V 475 17.652 82.489 148.614 1.00967.66 S ATOM 13485 SG CYS V 504 16.190 80.918 145.883 1.00984.89 S ATOM 13511 SG CYS V 507 14.129 81.711 148.569 1.00981.96 S ATOM 17069 SG CYS U 494 64.232 110.167 156.068 1.00795.71 S ATOM 17089 SG CYS U 497 60.555 110.120 154.255 1.00862.15 S ATOM 17211 SG CYS U 514 61.098 107.970 157.479 1.00852.40 S ATOM 17234 SG CYS U 517 62.294 107.141 154.749 1.00888.10 S ATOM 17402 SG CYS U 537 68.963 105.971 145.777 1.00964.65 S ATOM 17423 SG CYS U 540 65.335 107.141 147.220 1.00939.52 S ATOM 17560 SG CYS U 559 66.978 108.496 144.003 1.00853.47 S ATOM 17582 SG CYS U 562 67.664 109.848 146.790 1.00782.87 S ATOM 17486 SG CYS U 549 80.325 102.528 141.482 1.00920.09 S ATOM 17520 SG CYS U 554 80.010 100.301 144.299 1.00854.55 S ATOM 17733 SG CYS U 583 79.387 104.089 144.653 1.00866.46 S ATOM 17759 SG CYS U 586 82.701 102.384 145.094 1.00862.36 S ATOM 20473 SG CYS Y 494 76.077 25.554 106.318 1.00619.87 S ATOM 20493 SG CYS Y 497 74.050 27.796 103.241 1.00659.34 S ATOM 20615 SG CYS Y 514 77.714 28.224 103.957 1.00617.10 S ATOM 20638 SG CYS Y 517 75.416 29.522 105.503 1.00620.56 S ATOM 20806 SG CYS Y 537 68.419 30.353 114.241 1.00730.33 S ATOM 20827 SG CYS Y 540 68.458 30.668 110.382 1.00713.74 S ATOM 20964 SG CYS Y 559 65.192 29.810 112.182 1.00725.86 S ATOM 20986 SG CYS Y 562 67.728 27.374 111.511 1.00701.19 S ATOM 20890 SG CYS Y 549 66.897 30.914 127.154 1.00703.29 S ATOM 20924 SG CYS Y 554 70.109 32.264 127.104 1.00612.90 S ATOM 21137 SG CYS Y 583 69.333 28.412 125.957 1.00682.05 S ATOM 21163 SG CYS Y 586 70.245 28.835 129.055 1.00649.03 S Time building chain proxies: 5.55, per 1000 atoms: 0.23 Number of scatterers: 23771 At special positions: 0 Unit cell: (133.4, 150.88, 205.16, 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 9 29.99 S 116 16.00 P 330 15.00 O 4998 8.00 N 4349 7.00 C 13969 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: 2.11 Conformation dependent library (CDL) restraints added in 902.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN U1001 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 517 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 494 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 514 " pdb="ZN ZN U1001 " - pdb=" SG CYS U 497 " pdb=" ZN U1002 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 537 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 562 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 540 " pdb="ZN ZN U1002 " - pdb=" SG CYS U 559 " pdb=" ZN U1003 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 554 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 583 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 549 " pdb="ZN ZN U1003 " - pdb=" SG CYS U 586 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 435 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 418 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 415 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 438 " pdb=" ZN V1002 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 458 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 483 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 461 " pdb="ZN ZN V1002 " - pdb=" SG CYS V 480 " pdb=" ZN V1003 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 504 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 475 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 470 " pdb="ZN ZN V1003 " - pdb=" SG CYS V 507 " pdb=" ZN Y1001 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 494 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 497 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 514 " pdb="ZN ZN Y1001 " - pdb=" SG CYS Y 517 " pdb=" ZN Y1002 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 562 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 537 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 540 " pdb="ZN ZN Y1002 " - pdb=" SG CYS Y 559 " pdb=" ZN Y1003 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 583 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 549 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 554 " pdb="ZN ZN Y1003 " - pdb=" SG CYS Y 586 " Number of angles added : 54 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 21 sheets defined 50.2% alpha, 7.2% beta 163 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.629A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.727A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.030A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.610A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.633A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.624A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.641A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.328A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.557A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.538A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.616A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.815A pdb=" N GLN E 55 " --> pdb=" O ILE E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.565A pdb=" N ILE E 74 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.721A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.632A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.887A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.627A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.510A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.695A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.384A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.551A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.621A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.508A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.579A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 741 through 746 removed outlier: 3.733A pdb=" N LYS L 745 " --> pdb=" O GLY L 741 " (cutoff:3.500A) Processing helix chain 'V' and resid 396 through 407 removed outlier: 3.928A pdb=" N ALA V 405 " --> pdb=" O ALA V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 445 Processing helix chain 'V' and resid 481 through 487 Processing helix chain 'V' and resid 491 through 499 removed outlier: 4.027A pdb=" N LEU V 498 " --> pdb=" O ALA V 494 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 532 Processing helix chain 'V' and resid 565 through 575 Processing helix chain 'V' and resid 589 through 598 removed outlier: 3.782A pdb=" N VAL V 593 " --> pdb=" O GLU V 589 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL V 596 " --> pdb=" O ALA V 592 " (cutoff:3.500A) Processing helix chain 'V' and resid 613 through 620 removed outlier: 3.811A pdb=" N GLU V 617 " --> pdb=" O LYS V 613 " (cutoff:3.500A) Processing helix chain 'V' and resid 650 through 663 removed outlier: 3.525A pdb=" N GLU V 654 " --> pdb=" O ARG V 650 " (cutoff:3.500A) Processing helix chain 'V' and resid 683 through 695 Processing helix chain 'V' and resid 751 through 760 removed outlier: 4.424A pdb=" N VAL V 755 " --> pdb=" O TRP V 751 " (cutoff:3.500A) Processing helix chain 'V' and resid 760 through 766 removed outlier: 3.889A pdb=" N LYS V 764 " --> pdb=" O PHE V 760 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP V 765 " --> pdb=" O ALA V 761 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR V 766 " --> pdb=" O PRO V 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 760 through 766' Processing helix chain 'Z' and resid 565 through 574 Processing helix chain 'Z' and resid 587 through 598 removed outlier: 3.703A pdb=" N ILE Z 591 " --> pdb=" O CYS Z 587 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS Z 598 " --> pdb=" O GLY Z 594 " (cutoff:3.500A) Processing helix chain 'Z' and resid 612 through 620 Processing helix chain 'Z' and resid 645 through 663 Processing helix chain 'Z' and resid 683 through 695 Processing helix chain 'Z' and resid 741 through 746 removed outlier: 3.990A pdb=" N LYS Z 745 " --> pdb=" O GLY Z 741 " (cutoff:3.500A) Processing helix chain 'Z' and resid 753 through 760 removed outlier: 3.502A pdb=" N LEU Z 759 " --> pdb=" O VAL Z 755 " (cutoff:3.500A) Processing helix chain 'Z' and resid 760 through 767 Processing helix chain 'U' and resid 477 through 485 Processing helix chain 'U' and resid 489 through 493 removed outlier: 3.521A pdb=" N ILE U 493 " --> pdb=" O ILE U 490 " (cutoff:3.500A) Processing helix chain 'U' and resid 514 through 525 Processing helix chain 'U' and resid 560 through 567 Processing helix chain 'U' and resid 570 through 578 Processing helix chain 'U' and resid 600 through 611 removed outlier: 3.628A pdb=" N PHE U 609 " --> pdb=" O LEU U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 627 through 631 removed outlier: 3.571A pdb=" N ARG U 631 " --> pdb=" O ALA U 628 " (cutoff:3.500A) Processing helix chain 'U' and resid 644 through 654 removed outlier: 3.545A pdb=" N LEU U 648 " --> pdb=" O ALA U 644 " (cutoff:3.500A) Processing helix chain 'U' and resid 666 through 677 Processing helix chain 'U' and resid 691 through 698 Processing helix chain 'U' and resid 729 through 742 Processing helix chain 'U' and resid 762 through 774 Processing helix chain 'U' and resid 814 through 819 removed outlier: 3.662A pdb=" N CYS U 818 " --> pdb=" O GLU U 814 " (cutoff:3.500A) Processing helix chain 'U' and resid 860 through 868 Processing helix chain 'U' and resid 881 through 892 Processing helix chain 'U' and resid 894 through 903 Processing helix chain 'U' and resid 904 through 908 removed outlier: 3.514A pdb=" N GLU U 907 " --> pdb=" O PRO U 904 " (cutoff:3.500A) Processing helix chain 'Y' and resid 477 through 484 Processing helix chain 'Y' and resid 489 through 493 removed outlier: 3.610A pdb=" N ILE Y 493 " --> pdb=" O ILE Y 490 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 525 Processing helix chain 'Y' and resid 560 through 566 Processing helix chain 'Y' and resid 571 through 578 Processing helix chain 'Y' and resid 600 through 611 removed outlier: 3.725A pdb=" N GLN Y 606 " --> pdb=" O PRO Y 602 " (cutoff:3.500A) Processing helix chain 'Y' and resid 644 through 654 removed outlier: 3.691A pdb=" N LEU Y 648 " --> pdb=" O ALA Y 644 " (cutoff:3.500A) Processing helix chain 'Y' and resid 666 through 677 Processing helix chain 'Y' and resid 691 through 698 Processing helix chain 'Y' and resid 729 through 742 removed outlier: 3.870A pdb=" N GLU Y 733 " --> pdb=" O ARG Y 729 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Y' and resid 814 through 819 removed outlier: 3.752A pdb=" N CYS Y 818 " --> pdb=" O GLU Y 814 " (cutoff:3.500A) Processing helix chain 'Y' and resid 860 through 869 Processing helix chain 'Y' and resid 881 through 892 Processing helix chain 'Y' and resid 894 through 903 Processing helix chain 'Y' and resid 904 through 908 removed outlier: 3.778A pdb=" N GLU Y 907 " --> pdb=" O PRO Y 904 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.177A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.266A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.821A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.662A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'V' and resid 467 through 469 removed outlier: 3.672A pdb=" N PHE V 479 " --> pdb=" O LEU V 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'V' and resid 512 through 513 Processing sheet with id=AB1, first strand: chain 'V' and resid 578 through 584 removed outlier: 5.627A pdb=" N ILE V 555 " --> pdb=" O VAL V 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS V 580 " --> pdb=" O ILE V 555 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER V 584 " --> pdb=" O SER V 559 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL V 625 " --> pdb=" O MET V 675 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLU V 677 " --> pdb=" O VAL V 625 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY V 627 " --> pdb=" O GLU V 677 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL V 679 " --> pdb=" O GLY V 627 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG V 713 " --> pdb=" O ILE V 701 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE V 701 " --> pdb=" O ARG V 713 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 603 through 605 removed outlier: 8.965A pdb=" N LYS Z 603 " --> pdb=" O GLY Z 579 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR Z 581 " --> pdb=" O LYS Z 603 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N VAL Z 605 " --> pdb=" O TYR Z 581 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA Z 583 " --> pdb=" O VAL Z 605 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE Z 555 " --> pdb=" O VAL Z 578 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS Z 580 " --> pdb=" O ILE Z 555 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL Z 557 " --> pdb=" O LYS Z 580 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL Z 582 " --> pdb=" O VAL Z 557 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL Z 625 " --> pdb=" O MET Z 675 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N GLU Z 677 " --> pdb=" O VAL Z 625 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLY Z 627 " --> pdb=" O GLU Z 677 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 504 through 505 Processing sheet with id=AB4, first strand: chain 'U' and resid 546 through 548 Processing sheet with id=AB5, first strand: chain 'U' and resid 591 through 592 Processing sheet with id=AB6, first strand: chain 'U' and resid 682 through 684 removed outlier: 9.008A pdb=" N MET U 682 " --> pdb=" O ASP U 658 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR U 660 " --> pdb=" O MET U 682 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL U 684 " --> pdb=" O TYR U 660 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA U 662 " --> pdb=" O VAL U 684 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE U 634 " --> pdb=" O VAL U 657 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG U 659 " --> pdb=" O ILE U 634 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY U 707 " --> pdb=" O LEU U 639 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL U 704 " --> pdb=" O LEU U 754 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N GLU U 756 " --> pdb=" O VAL U 704 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLY U 706 " --> pdb=" O GLU U 756 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N VAL U 758 " --> pdb=" O GLY U 706 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 823 through 825 removed outlier: 4.335A pdb=" N VAL U 850 " --> pdb=" O ASP U 857 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 504 through 505 Processing sheet with id=AB9, first strand: chain 'Y' and resid 546 through 548 Processing sheet with id=AC1, first strand: chain 'Y' and resid 591 through 592 Processing sheet with id=AC2, first strand: chain 'Y' and resid 682 through 684 removed outlier: 7.747A pdb=" N ILE Y 634 " --> pdb=" O ASP Y 658 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR Y 660 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL Y 636 " --> pdb=" O TYR Y 660 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA Y 662 " --> pdb=" O VAL Y 636 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER Y 638 " --> pdb=" O ALA Y 662 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY Y 707 " --> pdb=" O LEU Y 639 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Y 704 " --> pdb=" O LEU Y 754 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLU Y 756 " --> pdb=" O VAL Y 704 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY Y 706 " --> pdb=" O GLU Y 756 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N VAL Y 758 " --> pdb=" O GLY Y 706 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Y' and resid 824 through 825 removed outlier: 3.958A pdb=" N VAL Y 850 " --> pdb=" O ASP Y 857 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 424 hydrogen bonds 848 hydrogen bond angles 0 basepair planarities 163 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 6.31 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3928 1.33 - 1.45: 7902 1.45 - 1.57: 12285 1.57 - 1.69: 658 1.69 - 1.82: 162 Bond restraints: 24935 Sorted by residual: bond pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.487 -0.033 8.30e-03 1.45e+04 1.63e+01 bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.60e+01 bond pdb=" N ASP U 579 " pdb=" CA ASP U 579 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.51e+01 bond pdb=" N VAL U 785 " pdb=" CA VAL U 785 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.38e+01 bond pdb=" N ILE U 493 " pdb=" CA ILE U 493 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 24930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 25943 1.51 - 3.02: 7526 3.02 - 4.53: 1514 4.53 - 6.04: 110 6.04 - 7.55: 2 Bond angle restraints: 35095 Sorted by residual: angle pdb=" C SER V 752 " pdb=" N VAL V 753 " pdb=" CA VAL V 753 " ideal model delta sigma weight residual 120.33 125.15 -4.82 8.00e-01 1.56e+00 3.63e+01 angle pdb=" C SER Z 752 " pdb=" N VAL Z 753 " pdb=" CA VAL Z 753 " ideal model delta sigma weight residual 120.33 124.67 -4.34 8.00e-01 1.56e+00 2.95e+01 angle pdb=" O5' DA I 10 " pdb=" C5' DA I 10 " pdb=" C4' DA I 10 " ideal model delta sigma weight residual 109.40 113.20 -3.80 8.00e-01 1.56e+00 2.26e+01 angle pdb=" C VAL C 27 " pdb=" N GLY C 28 " pdb=" CA GLY C 28 " ideal model delta sigma weight residual 119.98 125.16 -5.18 1.11e+00 8.12e-01 2.18e+01 angle pdb=" C THR U 645 " pdb=" N GLY U 646 " pdb=" CA GLY U 646 " ideal model delta sigma weight residual 119.98 125.00 -5.02 1.11e+00 8.12e-01 2.04e+01 ... (remaining 35090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12616 35.99 - 71.99: 1394 71.99 - 107.98: 19 107.98 - 143.98: 0 143.98 - 179.97: 2 Dihedral angle restraints: 14031 sinusoidal: 7917 harmonic: 6114 Sorted by residual: dihedral pdb=" CA ASN V 422 " pdb=" C ASN V 422 " pdb=" N PRO V 423 " pdb=" CA PRO V 423 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLU U 523 " pdb=" C GLU U 523 " pdb=" N CYS U 524 " pdb=" CA CYS U 524 " ideal model delta harmonic sigma weight residual -180.00 -158.14 -21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" C4' DG J 180 " pdb=" C3' DG J 180 " pdb=" O3' DG J 180 " pdb=" P DC J 181 " ideal model delta sinusoidal sigma weight residual -140.00 39.97 -179.97 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 14028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2185 0.066 - 0.131: 1420 0.131 - 0.197: 244 0.197 - 0.262: 3 0.262 - 0.327: 2 Chirality restraints: 3854 Sorted by residual: chirality pdb=" C3' DG J 180 " pdb=" C4' DG J 180 " pdb=" O3' DG J 180 " pdb=" C2' DG J 180 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C3' DG I 3 " pdb=" C4' DG I 3 " pdb=" O3' DG I 3 " pdb=" C2' DG I 3 " both_signs ideal model delta sigma weight residual False -2.73 -2.42 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3851 not shown) Planarity restraints: 3352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 182 " -0.021 2.00e-02 2.50e+03 1.21e-02 3.31e+00 pdb=" N1 DC J 182 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DC J 182 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC J 182 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DC J 182 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 182 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 182 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 182 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 182 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 37 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C GLY C 37 " -0.031 2.00e-02 2.50e+03 pdb=" O GLY C 37 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN C 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 35 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ARG C 35 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG C 35 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS C 36 " -0.011 2.00e-02 2.50e+03 ... (remaining 3349 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 492 2.67 - 3.23: 18856 3.23 - 3.78: 40005 3.78 - 4.34: 51546 4.34 - 4.90: 77029 Nonbonded interactions: 187928 Sorted by model distance: nonbonded pdb=" NH2 ARG A 40 " pdb=" N3 DG J 265 " model vdw 2.110 3.200 nonbonded pdb=" OG SER U 663 " pdb=" O GLY U 685 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 304 " model vdw 2.363 3.040 nonbonded pdb=" NH1 ARG A 42 " pdb=" OP1 DC I 154 " model vdw 2.363 3.120 nonbonded pdb=" OE2 GLU A 133 " pdb=" NH2 ARG B 95 " model vdw 2.384 3.120 ... (remaining 187923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 111) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'U' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 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 : 0.011 0.046 24971 Z= 0.839 Angle : 1.497 28.005 35149 Z= 1.061 Chirality : 0.075 0.327 3854 Planarity : 0.002 0.021 3352 Dihedral : 21.442 179.973 10095 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -2.58 (0.15), residues: 2073 helix: -1.64 (0.13), residues: 987 sheet: -0.87 (0.43), residues: 115 loop : -1.80 (0.16), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 792 TYR 0.020 0.002 TYR A 99 PHE 0.020 0.002 PHE Z 652 TRP 0.014 0.002 TRP U 601 HIS 0.005 0.001 HIS V 758 Details of bonding type rmsd/Z covalent geometry : bond 0.01120 / 0.84 (24935) covalent geometry : angle 1.39293 / 1.06 (35095) hydrogen bonds : bond 0.17649 / 11.65 ( 1149) hydrogen bonds : angle 6.73203 / 4.75 ( 2957) metal coordination : bond 0.01263 / 0.80 ( 36) metal coordination : angle 14.05526 / 9.66 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9376 (mt-10) cc_final: 0.9136 (tm-30) REVERT: A 109 LEU cc_start: 0.9565 (mt) cc_final: 0.9201 (mm) REVERT: B 64 ASN cc_start: 0.9018 (m-40) cc_final: 0.8666 (t0) REVERT: C 33 LEU cc_start: 0.8665 (mt) cc_final: 0.8142 (mt) REVERT: C 108 LEU cc_start: 0.9401 (mt) cc_final: 0.9104 (pt) REVERT: D 41 VAL cc_start: 0.8967 (t) cc_final: 0.8716 (p) REVERT: D 51 ILE cc_start: 0.8859 (tt) cc_final: 0.5960 (tp) REVERT: D 68 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9041 (mm-30) REVERT: D 70 ILE cc_start: 0.9816 (mt) cc_final: 0.9544 (tp) REVERT: D 86 ILE cc_start: 0.9438 (mt) cc_final: 0.8977 (tp) REVERT: E 67 PHE cc_start: 0.8759 (t80) cc_final: 0.8278 (t80) REVERT: E 110 CYS cc_start: 0.9126 (m) cc_final: 0.8521 (t) REVERT: F 61 PHE cc_start: 0.9669 (t80) cc_final: 0.9438 (t80) REVERT: F 68 ASP cc_start: 0.9122 (m-30) cc_final: 0.8800 (m-30) REVERT: G 63 LEU cc_start: 0.9137 (mt) cc_final: 0.8918 (mt) REVERT: G 83 LEU cc_start: 0.9622 (mt) cc_final: 0.9415 (mp) REVERT: G 87 VAL cc_start: 0.9591 (t) cc_final: 0.9271 (p) REVERT: H 77 LEU cc_start: 0.9153 (mt) cc_final: 0.8825 (mt) REVERT: V 506 MET cc_start: 0.5189 (ttp) cc_final: 0.4874 (mmp) REVERT: U 761 MET cc_start: -0.2388 (ptm) cc_final: -0.2869 (ptt) REVERT: Y 801 MET cc_start: 0.0025 (ptm) cc_final: -0.0362 (ptt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1772 time to fit residues: 79.6102 Evaluate side-chains 162 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 0.1980 chunk 235 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN C 31 HIS C 68 ASN E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN U 527 GLN U 789 HIS U 821 HIS U 873 HIS U 900 HIS Y 789 HIS Y 900 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.077362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.050153 restraints weight = 217502.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051370 restraints weight = 143642.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.052140 restraints weight = 105250.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.052694 restraints weight = 84903.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.053020 restraints weight = 72592.823| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24971 Z= 0.166 Angle : 0.656 13.130 35149 Z= 0.361 Chirality : 0.042 0.235 3854 Planarity : 0.004 0.045 3352 Dihedral : 26.991 176.188 5929 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.06 % Allowed : 0.83 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.84 (0.17), residues: 2073 helix: 0.17 (0.15), residues: 992 sheet: -0.74 (0.40), residues: 132 loop : -1.27 (0.18), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG U 556 TYR 0.020 0.001 TYR G 57 PHE 0.021 0.002 PHE Z 652 TRP 0.009 0.001 TRP Y 860 HIS 0.005 0.001 HIS Z 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (24935) covalent geometry : angle 0.61855 / 0.36 (35095) hydrogen bonds : bond 0.05554 / 3.75 ( 1149) hydrogen bonds : angle 4.33701 / 3.11 ( 2957) metal coordination : bond 0.00844 / 0.62 ( 36) metal coordination : angle 5.59459 / 3.68 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.774 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: B 81 VAL cc_start: 0.8562 (t) cc_final: 0.8158 (p) REVERT: C 39 TYR cc_start: 0.7532 (m-80) cc_final: 0.7252 (m-80) REVERT: D 56 MET cc_start: 0.9167 (mmp) cc_final: 0.8888 (mmm) REVERT: D 70 ILE cc_start: 0.9501 (mt) cc_final: 0.9279 (tp) REVERT: D 86 ILE cc_start: 0.9132 (mt) cc_final: 0.8684 (tp) REVERT: E 61 LEU cc_start: 0.5048 (mt) cc_final: 0.4708 (mt) REVERT: E 94 GLU cc_start: 0.9271 (mm-30) cc_final: 0.9063 (mm-30) REVERT: E 110 CYS cc_start: 0.8511 (m) cc_final: 0.8045 (t) REVERT: G 87 VAL cc_start: 0.9169 (t) cc_final: 0.8963 (p) REVERT: H 70 ILE cc_start: 0.9191 (tp) cc_final: 0.8289 (tp) REVERT: H 98 LEU cc_start: 0.9458 (tt) cc_final: 0.8993 (tt) REVERT: U 864 MET cc_start: 0.8808 (mmp) cc_final: 0.8608 (mmt) REVERT: Y 801 MET cc_start: 0.3128 (ptm) cc_final: 0.2850 (ptt) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.1566 time to fit residues: 53.0063 Evaluate side-chains 147 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 185 optimal weight: 0.3980 chunk 199 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 187 optimal weight: 50.0000 chunk 193 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 85 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 31 HIS G 68 ASN H 106 HIS V 697 ASN U 527 GLN U 847 HIS Y 613 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.067335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.039362 restraints weight = 225300.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.040330 restraints weight = 142176.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.040885 restraints weight = 104975.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041342 restraints weight = 86822.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.041695 restraints weight = 75466.968| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 24971 Z= 0.287 Angle : 0.835 15.946 35149 Z= 0.464 Chirality : 0.047 0.317 3854 Planarity : 0.006 0.058 3352 Dihedral : 28.015 176.088 5929 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.44 % Allowed : 2.20 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.62 (0.17), residues: 2073 helix: 0.11 (0.15), residues: 999 sheet: -0.34 (0.40), residues: 140 loop : -0.90 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 128 TYR 0.066 0.002 TYR B 51 PHE 0.027 0.002 PHE H 67 TRP 0.009 0.001 TRP U 795 HIS 0.010 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.29 (24935) covalent geometry : angle 0.81938 / 0.46 (35095) hydrogen bonds : bond 0.12520 / 8.45 ( 1149) hydrogen bonds : angle 4.86582 / 3.55 ( 2957) metal coordination : bond 0.00667 / 0.47 ( 36) metal coordination : angle 4.12738 / 2.93 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.779 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: B 98 TYR cc_start: 0.8429 (m-10) cc_final: 0.8165 (m-10) REVERT: E 50 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8572 (mm-30) REVERT: E 74 ILE cc_start: 0.8625 (mt) cc_final: 0.8330 (tt) REVERT: E 110 CYS cc_start: 0.8831 (m) cc_final: 0.8190 (t) REVERT: F 74 GLU cc_start: 0.9428 (OUTLIER) cc_final: 0.9200 (pm20) REVERT: V 506 MET cc_start: 0.4196 (mmp) cc_final: 0.3352 (tmm) REVERT: U 864 MET cc_start: 0.8741 (mmp) cc_final: 0.8500 (mmt) outliers start: 8 outliers final: 4 residues processed: 179 average time/residue: 0.1550 time to fit residues: 45.3771 Evaluate side-chains 135 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 213 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 211 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 207 optimal weight: 40.0000 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.066299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037414 restraints weight = 224148.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.038401 restraints weight = 134896.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039053 restraints weight = 97262.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.039472 restraints weight = 78376.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.039685 restraints weight = 67972.547| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5858 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 24971 Z= 0.195 Angle : 0.662 9.671 35149 Z= 0.367 Chirality : 0.044 0.245 3854 Planarity : 0.005 0.101 3352 Dihedral : 28.466 175.423 5929 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.12 (0.17), residues: 2073 helix: 0.69 (0.16), residues: 997 sheet: -0.33 (0.41), residues: 141 loop : -0.83 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 29 TYR 0.049 0.002 TYR U 533 PHE 0.012 0.001 PHE D 67 TRP 0.008 0.001 TRP U 601 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (24935) covalent geometry : angle 0.64679 / 0.37 (35095) hydrogen bonds : bond 0.06482 / 4.34 ( 1149) hydrogen bonds : angle 4.28623 / 3.12 ( 2957) metal coordination : bond 0.00480 / 0.34 ( 36) metal coordination : angle 3.68468 / 2.67 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.780 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: A 62 ILE cc_start: 0.8806 (tp) cc_final: 0.8508 (tp) REVERT: A 99 TYR cc_start: 0.9239 (t80) cc_final: 0.9028 (t80) REVERT: A 119 ILE cc_start: 0.8991 (pt) cc_final: 0.8610 (pt) REVERT: D 51 ILE cc_start: 0.9098 (tt) cc_final: 0.8563 (tp) REVERT: E 74 ILE cc_start: 0.8682 (mt) cc_final: 0.8440 (tt) REVERT: E 110 CYS cc_start: 0.8772 (m) cc_final: 0.8031 (t) REVERT: V 506 MET cc_start: 0.4228 (mmp) cc_final: 0.3386 (tmm) REVERT: U 801 MET cc_start: 0.3492 (tmm) cc_final: 0.3184 (tmm) REVERT: U 852 MET cc_start: 0.2269 (ttt) cc_final: 0.1999 (tpt) REVERT: U 864 MET cc_start: 0.8721 (mmp) cc_final: 0.8501 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1496 time to fit residues: 38.8948 Evaluate side-chains 124 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 226 optimal weight: 50.0000 chunk 186 optimal weight: 8.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 610 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.062343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033927 restraints weight = 228728.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.034822 restraints weight = 136274.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.035323 restraints weight = 98348.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.035773 restraints weight = 80812.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035982 restraints weight = 69726.572| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 24971 Z= 0.252 Angle : 0.734 15.104 35149 Z= 0.408 Chirality : 0.045 0.377 3854 Planarity : 0.005 0.056 3352 Dihedral : 28.658 173.531 5929 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.11 % Allowed : 1.38 % Favored : 98.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.09 % 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: -0.18 (0.18), residues: 2073 helix: 0.58 (0.16), residues: 1001 sheet: -0.33 (0.42), residues: 133 loop : -0.77 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 29 TYR 0.029 0.002 TYR G 50 PHE 0.016 0.001 PHE B 100 TRP 0.007 0.001 TRP Y 601 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.25 (24935) covalent geometry : angle 0.72235 / 0.41 (35095) hydrogen bonds : bond 0.11664 / 7.86 ( 1149) hydrogen bonds : angle 4.53619 / 3.29 ( 2957) metal coordination : bond 0.01216 / 0.72 ( 36) metal coordination : angle 3.46956 / 2.29 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9229 (t80) cc_final: 0.9016 (t80) REVERT: E 74 ILE cc_start: 0.8476 (mt) cc_final: 0.8003 (tt) REVERT: E 107 THR cc_start: 0.8495 (m) cc_final: 0.8200 (m) REVERT: E 110 CYS cc_start: 0.8992 (m) cc_final: 0.8318 (t) REVERT: E 119 ILE cc_start: 0.8365 (pt) cc_final: 0.7445 (mm) REVERT: V 506 MET cc_start: 0.4537 (mmp) cc_final: 0.3762 (tmm) REVERT: V 700 MET cc_start: 0.8314 (mmp) cc_final: 0.8070 (mmp) REVERT: U 801 MET cc_start: 0.2913 (tmm) cc_final: 0.2676 (tmm) REVERT: U 864 MET cc_start: 0.8721 (mmp) cc_final: 0.8505 (mmp) outliers start: 2 outliers final: 1 residues processed: 145 average time/residue: 0.1455 time to fit residues: 35.4533 Evaluate side-chains 108 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 84 optimal weight: 50.0000 chunk 210 optimal weight: 50.0000 chunk 162 optimal weight: 9.9990 chunk 205 optimal weight: 0.1980 chunk 79 optimal weight: 20.0000 chunk 201 optimal weight: 50.0000 chunk 213 optimal weight: 30.0000 chunk 27 optimal weight: 0.8980 chunk 161 optimal weight: 50.0000 chunk 199 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 overall best weight: 12.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN G 84 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 710 HIS Y 886 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.054683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.028361 restraints weight = 248445.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.029003 restraints weight = 158910.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029412 restraints weight = 119897.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029689 restraints weight = 100098.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029824 restraints weight = 88330.160| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.8787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.155 24971 Z= 0.499 Angle : 1.161 20.180 35149 Z= 0.627 Chirality : 0.063 0.347 3854 Planarity : 0.009 0.122 3352 Dihedral : 30.417 173.044 5929 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 41.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 0.11 % Allowed : 2.15 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2073 helix: -0.95 (0.15), residues: 1003 sheet: -0.31 (0.44), residues: 131 loop : -0.95 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 63 TYR 0.060 0.003 TYR C 39 PHE 0.044 0.003 PHE A 84 TRP 0.014 0.002 TRP Y 893 HIS 0.019 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00905 / 0.50 (24935) covalent geometry : angle 1.14269 / 0.63 (35095) hydrogen bonds : bond 0.22078 / 14.72 ( 1149) hydrogen bonds : angle 6.38148 / 4.63 ( 2957) metal coordination : bond 0.01793 / 0.87 ( 36) metal coordination : angle 5.37452 / 3.81 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.792 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 99 TYR cc_start: 0.9353 (t80) cc_final: 0.9085 (t80) REVERT: C 111 ILE cc_start: 0.6042 (mp) cc_final: 0.5651 (mm) REVERT: E 120 MET cc_start: 0.6211 (tmm) cc_final: 0.5983 (tmm) REVERT: V 506 MET cc_start: 0.4784 (mmp) cc_final: 0.4094 (tmm) REVERT: U 801 MET cc_start: 0.2368 (tmm) cc_final: 0.2121 (tmm) REVERT: Y 779 MET cc_start: 0.3019 (tpt) cc_final: 0.2785 (tpt) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.1639 time to fit residues: 26.8137 Evaluate side-chains 78 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 145 optimal weight: 0.0170 chunk 82 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 36 optimal weight: 0.0170 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN F 25 ASN ** F 75 HIS ** 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 = 0.3481 r_free = 0.3481 target = 0.059776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.030791 restraints weight = 230616.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.031598 restraints weight = 132203.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032144 restraints weight = 94666.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.032414 restraints weight = 76415.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.032662 restraints weight = 67584.326| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.8417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24971 Z= 0.156 Angle : 0.742 10.685 35149 Z= 0.402 Chirality : 0.050 0.289 3854 Planarity : 0.004 0.048 3352 Dihedral : 30.498 170.835 5929 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: -0.32 (0.18), residues: 2073 helix: 0.44 (0.16), residues: 1003 sheet: -0.52 (0.43), residues: 131 loop : -0.79 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 55 TYR 0.032 0.002 TYR U 793 PHE 0.018 0.001 PHE U 794 TRP 0.018 0.001 TRP U 795 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (24935) covalent geometry : angle 0.72371 / 0.40 (35095) hydrogen bonds : bond 0.07778 / 5.19 ( 1149) hydrogen bonds : angle 4.56550 / 3.29 ( 2957) metal coordination : bond 0.01541 / 0.81 ( 36) metal coordination : angle 4.24906 / 2.95 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9314 (t80) cc_final: 0.9107 (t80) REVERT: A 107 THR cc_start: 0.9094 (m) cc_final: 0.8868 (m) REVERT: A 110 CYS cc_start: 0.9113 (m) cc_final: 0.8807 (p) REVERT: A 119 ILE cc_start: 0.9285 (pt) cc_final: 0.9063 (pt) REVERT: E 94 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9343 (mm-30) REVERT: E 110 CYS cc_start: 0.9339 (m) cc_final: 0.8776 (t) REVERT: F 68 ASP cc_start: 0.9393 (m-30) cc_final: 0.9105 (p0) REVERT: V 506 MET cc_start: 0.4675 (mmp) cc_final: 0.4037 (tmm) REVERT: U 801 MET cc_start: 0.3796 (tmm) cc_final: 0.2734 (ptt) REVERT: Y 761 MET cc_start: 0.3346 (mmp) cc_final: 0.2935 (mtt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1390 time to fit residues: 30.6081 Evaluate side-chains 97 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 120 optimal weight: 40.0000 chunk 234 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 180 optimal weight: 50.0000 chunk 201 optimal weight: 10.0000 chunk 210 optimal weight: 50.0000 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 173 optimal weight: 40.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029694 restraints weight = 245834.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.030439 restraints weight = 142968.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030945 restraints weight = 102370.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.031262 restraints weight = 83218.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.031419 restraints weight = 73098.239| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24971 Z= 0.203 Angle : 0.720 10.962 35149 Z= 0.396 Chirality : 0.046 0.276 3854 Planarity : 0.005 0.073 3352 Dihedral : 30.072 169.000 5929 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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 (0.18), residues: 2073 helix: 0.49 (0.16), residues: 1003 sheet: -0.57 (0.43), residues: 131 loop : -0.70 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG U 823 TYR 0.036 0.002 TYR E 54 PHE 0.025 0.001 PHE U 868 TRP 0.011 0.001 TRP U 601 HIS 0.012 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.20 (24935) covalent geometry : angle 0.70138 / 0.39 (35095) hydrogen bonds : bond 0.10526 / 7.09 ( 1149) hydrogen bonds : angle 4.66780 / 3.37 ( 2957) metal coordination : bond 0.00591 / 0.40 ( 36) metal coordination : angle 4.16542 / 2.89 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9373 (t80) cc_final: 0.9092 (t80) REVERT: A 107 THR cc_start: 0.9259 (m) cc_final: 0.9020 (m) REVERT: A 110 CYS cc_start: 0.9205 (m) cc_final: 0.8861 (p) REVERT: E 110 CYS cc_start: 0.9426 (m) cc_final: 0.8922 (t) REVERT: F 68 ASP cc_start: 0.9469 (m-30) cc_final: 0.9195 (p0) REVERT: V 506 MET cc_start: 0.4657 (mmp) cc_final: 0.4028 (tmm) REVERT: U 801 MET cc_start: 0.3591 (tmm) cc_final: 0.2255 (ptt) REVERT: U 864 MET cc_start: 0.8762 (tpt) cc_final: 0.8318 (mmm) REVERT: Y 852 MET cc_start: 0.5958 (mtp) cc_final: 0.5741 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1454 time to fit residues: 26.2700 Evaluate side-chains 83 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 40.0000 chunk 222 optimal weight: 0.6980 chunk 177 optimal weight: 40.0000 chunk 120 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 109 optimal weight: 30.0000 chunk 42 optimal weight: 0.1980 chunk 77 optimal weight: 20.0000 chunk 36 optimal weight: 0.4980 chunk 209 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030677 restraints weight = 244145.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.031523 restraints weight = 136677.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.031958 restraints weight = 96086.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032361 restraints weight = 78804.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.032540 restraints weight = 68394.119| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6159 moved from start: 0.8680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24971 Z= 0.144 Angle : 0.662 9.966 35149 Z= 0.365 Chirality : 0.045 0.249 3854 Planarity : 0.004 0.052 3352 Dihedral : 29.861 171.939 5929 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.07 (0.18), residues: 2073 helix: 0.84 (0.16), residues: 1006 sheet: -0.59 (0.43), residues: 131 loop : -0.67 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 823 TYR 0.021 0.001 TYR E 54 PHE 0.017 0.001 PHE U 868 TRP 0.011 0.001 TRP U 601 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (24935) covalent geometry : angle 0.64425 / 0.36 (35095) hydrogen bonds : bond 0.06374 / 4.28 ( 1149) hydrogen bonds : angle 4.35828 / 3.13 ( 2957) metal coordination : bond 0.00536 / 0.37 ( 36) metal coordination : angle 3.91779 / 2.72 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9344 (t80) cc_final: 0.9077 (t80) REVERT: A 107 THR cc_start: 0.9085 (m) cc_final: 0.8840 (m) REVERT: A 110 CYS cc_start: 0.8988 (m) cc_final: 0.8669 (p) REVERT: A 119 ILE cc_start: 0.9257 (pt) cc_final: 0.8894 (pt) REVERT: B 68 ASP cc_start: 0.9671 (m-30) cc_final: 0.9340 (p0) REVERT: E 94 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9375 (mm-30) REVERT: E 110 CYS cc_start: 0.9339 (m) cc_final: 0.8810 (t) REVERT: F 43 VAL cc_start: 0.5325 (t) cc_final: 0.5125 (t) REVERT: F 68 ASP cc_start: 0.9426 (m-30) cc_final: 0.9138 (p0) REVERT: V 506 MET cc_start: 0.4971 (mmp) cc_final: 0.4362 (tmm) REVERT: U 801 MET cc_start: 0.3596 (tmm) cc_final: 0.1825 (ptt) REVERT: U 864 MET cc_start: 0.8912 (tpt) cc_final: 0.8480 (mmt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1386 time to fit residues: 27.3004 Evaluate side-chains 93 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 169 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 136 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.058937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030251 restraints weight = 244738.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.031094 restraints weight = 137304.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.031628 restraints weight = 96610.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.031933 restraints weight = 78272.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.032087 restraints weight = 68567.590| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.8873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24971 Z= 0.159 Angle : 0.655 16.175 35149 Z= 0.361 Chirality : 0.044 0.250 3854 Planarity : 0.004 0.058 3352 Dihedral : 29.613 172.556 5929 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % 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: 0.16 (0.18), residues: 2073 helix: 0.90 (0.16), residues: 1004 sheet: -0.49 (0.44), residues: 121 loop : -0.60 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 69 TYR 0.027 0.001 TYR E 54 PHE 0.013 0.001 PHE U 868 TRP 0.010 0.001 TRP U 601 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (24935) covalent geometry : angle 0.63851 / 0.36 (35095) hydrogen bonds : bond 0.07852 / 5.30 ( 1149) hydrogen bonds : angle 4.33528 / 3.12 ( 2957) metal coordination : bond 0.00503 / 0.35 ( 36) metal coordination : angle 3.77234 / 2.63 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9357 (t80) cc_final: 0.9064 (t80) REVERT: A 119 ILE cc_start: 0.9235 (pt) cc_final: 0.8915 (pt) REVERT: C 64 GLU cc_start: 0.9105 (pp20) cc_final: 0.8893 (pp20) REVERT: E 94 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9366 (mm-30) REVERT: E 110 CYS cc_start: 0.9333 (m) cc_final: 0.8892 (t) REVERT: F 68 ASP cc_start: 0.9437 (m-30) cc_final: 0.9172 (p0) REVERT: V 506 MET cc_start: 0.5132 (mmp) cc_final: 0.4505 (tmm) REVERT: Z 700 MET cc_start: 0.5296 (mmp) cc_final: 0.5018 (mmp) REVERT: U 801 MET cc_start: 0.3742 (tmm) cc_final: 0.3321 (tmm) REVERT: Y 852 MET cc_start: 0.5935 (mtp) cc_final: 0.5726 (mmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1459 time to fit residues: 27.9283 Evaluate side-chains 96 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 206 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 185 optimal weight: 30.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 395 GLN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 612 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.055944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028437 restraints weight = 258413.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029176 restraints weight = 150822.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.029640 restraints weight = 108258.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029929 restraints weight = 88032.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.030070 restraints weight = 77268.814| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.9657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24971 Z= 0.280 Angle : 0.800 12.146 35149 Z= 0.440 Chirality : 0.049 0.292 3854 Planarity : 0.006 0.072 3352 Dihedral : 30.017 173.628 5929 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.43 (0.18), residues: 2073 helix: 0.18 (0.16), residues: 1009 sheet: -0.62 (0.44), residues: 121 loop : -0.63 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG U 823 TYR 0.028 0.002 TYR E 54 PHE 0.022 0.002 PHE E 84 TRP 0.011 0.001 TRP U 795 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.28 (24935) covalent geometry : angle 0.78587 / 0.44 (35095) hydrogen bonds : bond 0.14006 / 9.42 ( 1149) hydrogen bonds : angle 5.09395 / 3.66 ( 2957) metal coordination : bond 0.00583 / 0.41 ( 36) metal coordination : angle 3.89010 / 2.71 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5814.59 seconds wall clock time: 100 minutes 27.63 seconds (6027.63 seconds total)