Starting phenix.real_space_refine on Fri Feb 6 09:10:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3u_47496/02_2026/9e3u_47496.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3u_47496/02_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_47496/02_2026/9e3u_47496.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3u_47496/02_2026/9e3u_47496.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3u_47496/02_2026/9e3u_47496.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3u_47496/02_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-2.0-5952/lib/python3.9/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: 5.48, 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: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.44 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: 6.42 Time building geometry restraints manager: 2.80 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 - 1.45: 25468 1.45 - 2.90: 7769 2.90 - 4.35: 1685 4.35 - 5.80: 168 5.80 - 7.25: 5 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=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " ideal model delta sigma weight residual 110.00 117.25 -7.25 1.50e+00 4.44e-01 2.34e+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=" O3' DG J 331 " pdb=" C3' DG J 331 " pdb=" C2' DG J 331 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+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 - 0.051: 1895 0.051 - 0.103: 1397 0.103 - 0.154: 475 0.154 - 0.206: 84 0.206 - 0.257: 3 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 -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.65e+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 -2.66 -2.42 -0.24 2.00e-01 2.50e+01 1.47e+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: 11.830 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.130 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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= 0.834 Angle : 1.505 28.005 35149 Z= 1.048 Chirality : 0.071 0.257 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 covalent geometry : bond 0.01132 (24935) covalent geometry : angle 1.40193 (35095) hydrogen bonds : bond 0.17649 ( 1149) hydrogen bonds : angle 6.73203 ( 2957) metal coordination : bond 0.01263 ( 36) metal coordination : angle 14.05526 ( 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 : 0.802 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: 0.1931 time to fit residues: 86.0433 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 : 0.826 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN C 31 HIS C 68 ASN E 39 HIS V 697 ASN U 515 GLN U 613 HIS U 789 HIS U 821 HIS U 847 HIS U 873 HIS U 900 HIS Y 789 HIS Y 900 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.075204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.047557 restraints weight = 218115.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.048664 restraints weight = 140770.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.049491 restraints weight = 103621.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.050042 restraints weight = 82633.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.050363 restraints weight = 70344.827| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24971 Z= 0.176 Angle : 0.607 11.327 35149 Z= 0.334 Chirality : 0.036 0.151 3854 Planarity : 0.004 0.052 3352 Dihedral : 26.862 178.487 5929 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.06 % Allowed : 1.21 % Favored : 98.73 % 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: -0.31 (0.17), residues: 2073 helix: 0.70 (0.16), residues: 1000 sheet: -0.92 (0.39), residues: 138 loop : -1.05 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 441 TYR 0.023 0.002 TYR D 34 PHE 0.023 0.002 PHE G 25 TRP 0.009 0.001 TRP Y 795 HIS 0.006 0.001 HIS Z 657 Details of bonding type rmsd covalent geometry : bond 0.00375 (24935) covalent geometry : angle 0.58559 (35095) hydrogen bonds : bond 0.05345 ( 1149) hydrogen bonds : angle 3.99234 ( 2957) metal coordination : bond 0.00550 ( 36) metal coordination : angle 4.16067 ( 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 : 0.950 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 110 CYS cc_start: 0.8571 (m) cc_final: 0.8265 (t) REVERT: A 119 ILE cc_start: 0.8003 (pt) cc_final: 0.7695 (pt) REVERT: B 53 GLU cc_start: 0.8897 (mp0) cc_final: 0.8679 (mp0) REVERT: B 58 LEU cc_start: 0.9249 (pp) cc_final: 0.9018 (pp) REVERT: D 51 ILE cc_start: 0.8725 (tt) cc_final: 0.8075 (mp) REVERT: D 56 MET cc_start: 0.9383 (mmp) cc_final: 0.9120 (mmm) REVERT: D 70 ILE cc_start: 0.9576 (mt) cc_final: 0.9362 (tp) REVERT: D 77 LEU cc_start: 0.9082 (mt) cc_final: 0.8791 (mt) REVERT: D 86 ILE cc_start: 0.9114 (mt) cc_final: 0.8608 (tp) REVERT: D 115 VAL cc_start: 0.8738 (p) cc_final: 0.8488 (p) REVERT: E 110 CYS cc_start: 0.8673 (m) cc_final: 0.8097 (t) REVERT: H 58 ILE cc_start: 0.9589 (mm) cc_final: 0.9354 (tp) REVERT: H 70 ILE cc_start: 0.9320 (tp) cc_final: 0.8503 (tp) REVERT: H 77 LEU cc_start: 0.8819 (mt) cc_final: 0.8603 (mt) REVERT: H 98 LEU cc_start: 0.9389 (tt) cc_final: 0.8651 (tt) REVERT: V 700 MET cc_start: 0.8267 (mmt) cc_final: 0.7838 (mmp) REVERT: U 852 MET cc_start: 0.1208 (ttt) cc_final: 0.0869 (tpp) REVERT: U 864 MET cc_start: 0.8776 (mmp) cc_final: 0.8501 (mmt) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.1605 time to fit residues: 54.6867 Evaluate side-chains 144 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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: 30.0000 chunk 199 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 110 ASN D 106 HIS G 31 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 613 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.060008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032328 restraints weight = 240930.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.033233 restraints weight = 148380.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.033701 restraints weight = 107557.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.033994 restraints weight = 88241.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034242 restraints weight = 78224.606| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 24971 Z= 0.439 Angle : 0.908 13.427 35149 Z= 0.514 Chirality : 0.051 0.348 3854 Planarity : 0.008 0.107 3352 Dihedral : 28.613 178.032 5929 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 23.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.33 % Allowed : 2.48 % Favored : 97.19 % 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: -0.88 (0.17), residues: 2073 helix: -0.20 (0.16), residues: 996 sheet: -0.56 (0.39), residues: 141 loop : -0.88 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 29 TYR 0.045 0.003 TYR G 50 PHE 0.026 0.002 PHE F 61 TRP 0.011 0.001 TRP Y 601 HIS 0.013 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00937 (24935) covalent geometry : angle 0.88983 (35095) hydrogen bonds : bond 0.14887 ( 1149) hydrogen bonds : angle 5.47399 ( 2957) metal coordination : bond 0.00743 ( 36) metal coordination : angle 4.71022 ( 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 151 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9326 (t80) cc_final: 0.9066 (t80) REVERT: A 107 THR cc_start: 0.9113 (m) cc_final: 0.8868 (m) REVERT: A 110 CYS cc_start: 0.9121 (m) cc_final: 0.8782 (p) REVERT: B 40 ARG cc_start: 0.9146 (ttm170) cc_final: 0.8878 (mtp85) REVERT: C 110 ASN cc_start: 0.7354 (m110) cc_final: 0.7150 (m-40) REVERT: E 74 ILE cc_start: 0.8706 (mt) cc_final: 0.8415 (tt) REVERT: E 110 CYS cc_start: 0.9089 (m) cc_final: 0.8457 (t) REVERT: E 124 ILE cc_start: 0.8713 (pt) cc_final: 0.8503 (pt) REVERT: F 68 ASP cc_start: 0.9230 (m-30) cc_final: 0.8795 (p0) REVERT: V 506 MET cc_start: 0.4289 (mmp) cc_final: 0.3445 (tmm) REVERT: V 700 MET cc_start: 0.8420 (mmt) cc_final: 0.7660 (mmp) REVERT: Z 645 TYR cc_start: 0.8055 (p90) cc_final: 0.7692 (t80) REVERT: U 801 MET cc_start: 0.4023 (tmm) cc_final: 0.2648 (ptt) REVERT: U 852 MET cc_start: 0.2529 (ttt) cc_final: 0.2251 (tpt) REVERT: U 864 MET cc_start: 0.8753 (mmp) cc_final: 0.8546 (mmm) REVERT: Y 864 MET cc_start: 0.9273 (ptt) cc_final: 0.9040 (tpp) outliers start: 6 outliers final: 3 residues processed: 149 average time/residue: 0.1600 time to fit residues: 38.6477 Evaluate side-chains 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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: 9.9990 chunk 39 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN C 110 ASN D 44 GLN F 25 ASN G 68 ASN V 610 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.062716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.033473 restraints weight = 225485.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.034333 restraints weight = 134375.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034883 restraints weight = 96363.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035286 restraints weight = 78085.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.035466 restraints weight = 67951.345| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.6589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24971 Z= 0.164 Angle : 0.608 9.432 35149 Z= 0.338 Chirality : 0.038 0.140 3854 Planarity : 0.004 0.045 3352 Dihedral : 28.775 178.962 5929 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.03 (0.18), residues: 2073 helix: 0.80 (0.16), residues: 1005 sheet: -0.53 (0.40), residues: 140 loop : -0.78 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Y 823 TYR 0.015 0.001 TYR H 37 PHE 0.014 0.001 PHE Z 652 TRP 0.012 0.001 TRP U 795 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (24935) covalent geometry : angle 0.58856 (35095) hydrogen bonds : bond 0.05684 ( 1149) hydrogen bonds : angle 4.15134 ( 2957) metal coordination : bond 0.00458 ( 36) metal coordination : angle 3.90522 ( 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 151 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.844 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: 0.9270 (t80) cc_final: 0.9038 (t80) REVERT: A 110 CYS cc_start: 0.8903 (m) cc_final: 0.8591 (p) REVERT: D 51 ILE cc_start: 0.9158 (tt) cc_final: 0.8885 (tp) REVERT: E 74 ILE cc_start: 0.8618 (mt) cc_final: 0.7902 (tt) REVERT: E 110 CYS cc_start: 0.9030 (m) cc_final: 0.8386 (t) REVERT: F 43 VAL cc_start: 0.5029 (t) cc_final: 0.4618 (t) REVERT: V 506 MET cc_start: 0.4284 (mmp) cc_final: 0.3486 (tmm) REVERT: Z 645 TYR cc_start: 0.8044 (p90) cc_final: 0.7687 (t80) REVERT: U 801 MET cc_start: 0.3950 (tmm) cc_final: 0.2751 (ptt) REVERT: U 852 MET cc_start: 0.2529 (ttt) cc_final: 0.2272 (tpt) REVERT: U 864 MET cc_start: 0.8717 (mmp) cc_final: 0.8499 (mmm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1477 time to fit residues: 37.5780 Evaluate side-chains 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 50.0000 chunk 66 optimal weight: 0.9980 chunk 179 optimal weight: 30.0000 chunk 38 optimal weight: 10.0000 chunk 108 optimal weight: 50.0000 chunk 161 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 226 optimal weight: 50.0000 chunk 186 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.058074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030134 restraints weight = 239432.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.030877 restraints weight = 146403.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.031364 restraints weight = 107909.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.031608 restraints weight = 88478.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.031840 restraints weight = 78694.623| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.7970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 24971 Z= 0.358 Angle : 0.739 12.054 35149 Z= 0.416 Chirality : 0.043 0.195 3854 Planarity : 0.006 0.075 3352 Dihedral : 29.080 178.781 5929 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.06 % Allowed : 1.43 % Favored : 98.51 % 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: -0.20 (0.18), residues: 2073 helix: 0.49 (0.16), residues: 1003 sheet: -0.42 (0.41), residues: 140 loop : -0.68 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.049 0.002 TYR C 50 PHE 0.019 0.002 PHE F 100 TRP 0.009 0.001 TRP U 795 HIS 0.011 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00767 (24935) covalent geometry : angle 0.72151 (35095) hydrogen bonds : bond 0.12130 ( 1149) hydrogen bonds : angle 4.85159 ( 2957) metal coordination : bond 0.00773 ( 36) metal coordination : angle 4.14417 ( 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 121 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 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: A 99 TYR cc_start: 0.9319 (t80) cc_final: 0.9038 (t80) REVERT: A 107 THR cc_start: 0.9305 (m) cc_final: 0.9063 (m) REVERT: A 110 CYS cc_start: 0.9121 (m) cc_final: 0.8762 (p) REVERT: C 64 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8725 (mp0) REVERT: C 111 ILE cc_start: 0.6530 (mp) cc_final: 0.6126 (mm) REVERT: D 73 GLU cc_start: 0.9118 (mp0) cc_final: 0.8902 (mp0) REVERT: E 110 CYS cc_start: 0.9260 (m) cc_final: 0.8642 (t) REVERT: E 120 MET cc_start: 0.5784 (tmm) cc_final: 0.5547 (tmm) REVERT: F 68 ASP cc_start: 0.9326 (m-30) cc_final: 0.9046 (p0) REVERT: V 506 MET cc_start: 0.4694 (mmp) cc_final: 0.3938 (tmm) REVERT: Z 645 TYR cc_start: 0.8020 (p90) cc_final: 0.7792 (p90) REVERT: Z 700 MET cc_start: 0.6224 (pmm) cc_final: 0.5439 (mmp) REVERT: U 801 MET cc_start: 0.4277 (tmm) cc_final: 0.2829 (ptt) REVERT: U 864 MET cc_start: 0.8750 (mmp) cc_final: 0.8526 (mmp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1519 time to fit residues: 30.7181 Evaluate side-chains 89 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 10.0000 chunk 210 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 205 optimal weight: 40.0000 chunk 79 optimal weight: 1.9990 chunk 201 optimal weight: 50.0000 chunk 213 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 161 optimal weight: 40.0000 chunk 199 optimal weight: 40.0000 chunk 167 optimal weight: 40.0000 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 110 ASN H 64 ASN Y 534 GLN Y 886 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.057518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029319 restraints weight = 253465.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.030132 restraints weight = 144287.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030635 restraints weight = 102460.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.030889 restraints weight = 82953.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.031115 restraints weight = 73283.870| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.9039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 24971 Z= 0.273 Angle : 0.703 12.183 35149 Z= 0.393 Chirality : 0.041 0.200 3854 Planarity : 0.005 0.070 3352 Dihedral : 29.878 177.334 5929 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: -0.10 (0.18), residues: 2073 helix: 0.65 (0.16), residues: 1010 sheet: -0.49 (0.41), residues: 139 loop : -0.72 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG V 553 TYR 0.026 0.002 TYR E 54 PHE 0.014 0.001 PHE E 78 TRP 0.011 0.001 TRP U 601 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00562 (24935) covalent geometry : angle 0.68579 (35095) hydrogen bonds : bond 0.07990 ( 1149) hydrogen bonds : angle 4.58517 ( 2957) metal coordination : bond 0.00705 ( 36) metal coordination : angle 4.00606 ( 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 112 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 CYS cc_start: 0.9158 (m) cc_final: 0.8831 (p) REVERT: C 64 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8709 (mp0) REVERT: D 51 ILE cc_start: 0.9204 (tt) cc_final: 0.8983 (tt) REVERT: E 110 CYS cc_start: 0.9221 (m) cc_final: 0.8730 (t) REVERT: F 68 ASP cc_start: 0.9382 (m-30) cc_final: 0.9098 (p0) REVERT: V 506 MET cc_start: 0.4677 (mmp) cc_final: 0.4056 (tmm) REVERT: Z 645 TYR cc_start: 0.7988 (p90) cc_final: 0.7776 (p90) REVERT: U 801 MET cc_start: 0.3909 (tmm) cc_final: 0.2636 (ptt) REVERT: U 864 MET cc_start: 0.8618 (mmp) cc_final: 0.8400 (mmp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.1499 time to fit residues: 28.4312 Evaluate side-chains 85 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 123 optimal weight: 40.0000 chunk 156 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN V 710 HIS Y 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.057532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.029255 restraints weight = 251195.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.030045 restraints weight = 142949.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.030545 restraints weight = 100443.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030802 restraints weight = 80816.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.031034 restraints weight = 71049.244| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.9339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24971 Z= 0.224 Angle : 0.635 9.479 35149 Z= 0.356 Chirality : 0.038 0.160 3854 Planarity : 0.004 0.046 3352 Dihedral : 29.595 178.233 5929 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.18 (0.18), residues: 2073 helix: 0.95 (0.16), residues: 1011 sheet: -0.30 (0.43), residues: 129 loop : -0.69 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 792 TYR 0.023 0.001 TYR C 50 PHE 0.012 0.001 PHE Z 652 TRP 0.010 0.001 TRP U 601 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00476 (24935) covalent geometry : angle 0.61781 (35095) hydrogen bonds : bond 0.08119 ( 1149) hydrogen bonds : angle 4.37691 ( 2957) metal coordination : bond 0.00873 ( 36) metal coordination : angle 3.84433 ( 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 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9248 (m) cc_final: 0.8950 (m) REVERT: A 110 CYS cc_start: 0.9142 (m) cc_final: 0.8866 (p) REVERT: C 64 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8668 (mp0) REVERT: D 51 ILE cc_start: 0.9191 (tt) cc_final: 0.8956 (tt) REVERT: D 73 GLU cc_start: 0.9067 (mp0) cc_final: 0.8842 (mp0) REVERT: E 110 CYS cc_start: 0.9197 (m) cc_final: 0.8683 (t) REVERT: E 120 MET cc_start: 0.6528 (tmm) cc_final: 0.6318 (tmm) REVERT: F 68 ASP cc_start: 0.9388 (m-30) cc_final: 0.9120 (p0) REVERT: V 506 MET cc_start: 0.4981 (mmp) cc_final: 0.4394 (tmm) REVERT: Z 645 TYR cc_start: 0.7995 (p90) cc_final: 0.7785 (p90) REVERT: Z 700 MET cc_start: 0.6056 (pmm) cc_final: 0.5319 (mmp) REVERT: U 801 MET cc_start: 0.3763 (tmm) cc_final: 0.2633 (ptt) REVERT: U 864 MET cc_start: 0.8607 (mmp) cc_final: 0.8385 (mmp) REVERT: Y 761 MET cc_start: 0.4313 (mpp) cc_final: 0.3750 (mpp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1401 time to fit residues: 26.1148 Evaluate side-chains 90 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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: 50.0000 chunk 20 optimal weight: 0.8980 chunk 120 optimal weight: 40.0000 chunk 234 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 180 optimal weight: 50.0000 chunk 201 optimal weight: 50.0000 chunk 210 optimal weight: 50.0000 chunk 101 optimal weight: 20.0000 chunk 30 optimal weight: 0.0030 chunk 173 optimal weight: 5.9990 overall best weight: 4.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 612 ASN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.056546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.028494 restraints weight = 255814.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029276 restraints weight = 143988.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.029763 restraints weight = 101665.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.030030 restraints weight = 81754.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.030244 restraints weight = 72040.004| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 1.0038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24971 Z= 0.248 Angle : 0.661 9.466 35149 Z= 0.369 Chirality : 0.039 0.173 3854 Planarity : 0.004 0.044 3352 Dihedral : 29.692 179.184 5929 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.10 (0.18), residues: 2073 helix: 0.85 (0.16), residues: 1019 sheet: -0.55 (0.43), residues: 130 loop : -0.65 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.027 0.002 TYR A 99 PHE 0.022 0.002 PHE F 61 TRP 0.010 0.001 TRP U 601 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00529 (24935) covalent geometry : angle 0.64522 (35095) hydrogen bonds : bond 0.08758 ( 1149) hydrogen bonds : angle 4.46766 ( 2957) metal coordination : bond 0.00671 ( 36) metal coordination : angle 3.76431 ( 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 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9235 (m) cc_final: 0.9012 (m) REVERT: A 110 CYS cc_start: 0.9095 (m) cc_final: 0.8798 (p) REVERT: D 73 GLU cc_start: 0.9095 (mp0) cc_final: 0.8791 (mp0) REVERT: E 110 CYS cc_start: 0.9371 (m) cc_final: 0.8999 (p) REVERT: E 120 MET cc_start: 0.6594 (tmm) cc_final: 0.6381 (tmm) REVERT: F 68 ASP cc_start: 0.9406 (m-30) cc_final: 0.9145 (p0) REVERT: V 506 MET cc_start: 0.5231 (mmp) cc_final: 0.4675 (tmm) REVERT: Z 700 MET cc_start: 0.6070 (pmm) cc_final: 0.5369 (mmp) REVERT: U 801 MET cc_start: 0.3663 (tmm) cc_final: 0.2193 (ptm) REVERT: U 864 MET cc_start: 0.8598 (mmp) cc_final: 0.8367 (mmp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1313 time to fit residues: 24.6241 Evaluate side-chains 85 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 2.9990 chunk 177 optimal weight: 50.0000 chunk 120 optimal weight: 50.0000 chunk 147 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 612 ASN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 886 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.056619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.028409 restraints weight = 255912.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.029202 restraints weight = 141416.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.029582 restraints weight = 98919.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.029963 restraints weight = 80751.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.030134 restraints weight = 69814.966| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 1.0416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24971 Z= 0.229 Angle : 0.636 8.763 35149 Z= 0.358 Chirality : 0.039 0.194 3854 Planarity : 0.004 0.047 3352 Dihedral : 29.677 178.986 5929 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: 0.25 (0.18), residues: 2073 helix: 1.01 (0.16), residues: 1018 sheet: -0.47 (0.44), residues: 130 loop : -0.64 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 67 TYR 0.050 0.001 TYR C 50 PHE 0.035 0.001 PHE E 104 TRP 0.010 0.001 TRP U 601 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (24935) covalent geometry : angle 0.62228 (35095) hydrogen bonds : bond 0.08023 ( 1149) hydrogen bonds : angle 4.36322 ( 2957) metal coordination : bond 0.00508 ( 36) metal coordination : angle 3.39846 ( 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 108 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9232 (m) cc_final: 0.8986 (m) REVERT: A 110 CYS cc_start: 0.9136 (m) cc_final: 0.8844 (p) REVERT: C 64 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8680 (mp0) REVERT: E 110 CYS cc_start: 0.9309 (m) cc_final: 0.8838 (t) REVERT: E 120 MET cc_start: 0.7040 (tmm) cc_final: 0.6768 (tmm) REVERT: F 68 ASP cc_start: 0.9416 (m-30) cc_final: 0.9163 (p0) REVERT: H 73 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8574 (pt0) REVERT: V 506 MET cc_start: 0.5355 (mmp) cc_final: 0.4792 (tmm) REVERT: Z 700 MET cc_start: 0.6126 (pmm) cc_final: 0.5470 (mmp) REVERT: U 801 MET cc_start: 0.3350 (tmm) cc_final: 0.2766 (ptt) REVERT: U 864 MET cc_start: 0.8595 (mmp) cc_final: 0.8368 (mmp) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1440 time to fit residues: 26.3813 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 : 0.661 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 50.0000 chunk 169 optimal weight: 50.0000 chunk 7 optimal weight: 0.9990 chunk 196 optimal weight: 40.0000 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 612 ASN ** U 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 879 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.057596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028947 restraints weight = 252198.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029720 restraints weight = 138334.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.030233 restraints weight = 95578.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030501 restraints weight = 76048.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.030743 restraints weight = 66261.946| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 1.0498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24971 Z= 0.171 Angle : 0.615 9.746 35149 Z= 0.342 Chirality : 0.038 0.182 3854 Planarity : 0.004 0.041 3352 Dihedral : 29.552 179.457 5929 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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 : 0.00 % 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: 0.46 (0.18), residues: 2073 helix: 1.25 (0.16), residues: 1019 sheet: -0.48 (0.45), residues: 130 loop : -0.60 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 792 TYR 0.024 0.001 TYR A 99 PHE 0.020 0.001 PHE E 104 TRP 0.011 0.001 TRP U 601 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00360 (24935) covalent geometry : angle 0.59898 (35095) hydrogen bonds : bond 0.06073 ( 1149) hydrogen bonds : angle 4.15399 ( 2957) metal coordination : bond 0.00476 ( 36) metal coordination : angle 3.55486 ( 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 110 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.750 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 107 THR cc_start: 0.9120 (m) cc_final: 0.8870 (m) REVERT: A 110 CYS cc_start: 0.9050 (m) cc_final: 0.8838 (p) REVERT: D 51 ILE cc_start: 0.9165 (tt) cc_final: 0.8955 (tt) REVERT: E 110 CYS cc_start: 0.9264 (m) cc_final: 0.8932 (p) REVERT: F 68 ASP cc_start: 0.9387 (m-30) cc_final: 0.9152 (p0) REVERT: H 73 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8470 (pt0) REVERT: Z 700 MET cc_start: 0.6191 (pmm) cc_final: 0.5548 (mmp) REVERT: U 801 MET cc_start: 0.3219 (tmm) cc_final: 0.2078 (ptt) REVERT: U 864 MET cc_start: 0.8576 (mmp) cc_final: 0.8352 (mmp) REVERT: Y 852 MET cc_start: 0.5989 (mmm) cc_final: 0.5774 (mmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1227 time to fit residues: 23.4050 Evaluate side-chains 90 residues out of total 1815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 30.0000 chunk 28 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.0980 chunk 81 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 185 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.057223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.028696 restraints weight = 251681.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029521 restraints weight = 136858.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.030009 restraints weight = 94735.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.030295 restraints weight = 75514.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.030512 restraints weight = 66124.032| |-----------------------------------------------------------------------------| r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 1.0733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24971 Z= 0.183 Angle : 0.604 8.456 35149 Z= 0.338 Chirality : 0.037 0.172 3854 Planarity : 0.004 0.040 3352 Dihedral : 29.371 179.580 5929 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.50 (0.18), residues: 2073 helix: 1.29 (0.16), residues: 1026 sheet: -0.51 (0.45), residues: 122 loop : -0.59 (0.20), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 792 TYR 0.023 0.001 TYR A 99 PHE 0.024 0.001 PHE E 104 TRP 0.009 0.001 TRP U 601 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (24935) covalent geometry : angle 0.59017 (35095) hydrogen bonds : bond 0.06576 ( 1149) hydrogen bonds : angle 4.11098 ( 2957) metal coordination : bond 0.00461 ( 36) metal coordination : angle 3.38329 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6359.91 seconds wall clock time: 109 minutes 36.86 seconds (6576.86 seconds total)