Starting phenix.real_space_refine on Sun Sep 29 18:18:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grm_34207/09_2024/8grm_34207.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10341 atoms to isotropic. 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 4 6.06 5 P 289 5.49 5 S 38 5.16 5 C 8805 2.51 5 N 2856 2.21 5 O 3423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15415 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 92} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "P" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1169 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 130} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6391 SG CYS M 39 41.225 89.870 60.488 1.00 36.05 S ATOM 6413 SG CYS M 42 37.771 87.794 58.649 1.00 38.01 S ATOM 6350 SG CYS M 34 45.303 77.408 52.391 1.00 28.86 S ATOM 6508 SG CYS M 53 42.351 79.379 51.567 1.00 36.39 S ATOM 6529 SG CYS M 56 44.443 77.373 48.319 1.00 36.87 S ATOM 7206 SG CYS N 51 67.205 82.068 57.667 1.00 35.68 S ATOM 7227 SG CYS N 54 70.266 83.831 55.992 1.00 38.12 S ATOM 7375 SG CYS N 72 66.888 82.641 53.908 1.00 30.84 S ATOM 7394 SG CYS N 75 69.602 79.730 55.415 1.00 30.00 S ATOM 7329 SG CYS N 67 56.883 74.476 65.266 1.00 24.81 S ATOM 7483 SG CYS N 87 60.911 75.821 64.242 1.00 27.17 S ATOM 7503 SG CYS N 90 58.841 77.321 67.718 1.00 32.49 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY O 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.25 residue: pdb=" N GLY O 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 76 " occ=0.25 Time building chain proxies: 8.93, per 1000 atoms: 0.58 Number of scatterers: 15415 At special positions: 0 Unit cell: (117.066, 117.066, 123.51, 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 4 29.99 S 38 16.00 P 289 15.00 O 3423 8.00 N 2856 7.00 C 8805 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: 3.78 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 42 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 53 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " Number of angles added : 12 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2252 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 52.6% alpha, 5.7% beta 128 base pairs and 268 stacking pairs defined. Time for finding SS restraints: 6.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.737A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.566A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.757A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.702A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.489A pdb=" N GLU C 61 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.534A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.637A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.658A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 66 " --> pdb=" O MET D 62 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.511A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.718A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.584A pdb=" N ARG E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.511A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 4.048A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 74 removed outlier: 3.770A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.667A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.489A pdb=" N GLU G 61 " --> pdb=" O TYR G 57 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.534A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.539A pdb=" N TYR H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.762A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU H 71 " --> pdb=" O ASN H 67 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG H 72 " --> pdb=" O ASP H 68 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 removed outlier: 3.788A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.807A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 47 removed outlier: 4.626A pdb=" N ARG M 45 " --> pdb=" O THR M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 83 removed outlier: 3.782A pdb=" N GLN M 76 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 81 " --> pdb=" O ASP M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 99 removed outlier: 3.636A pdb=" N MET M 91 " --> pdb=" O PHE M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 45 through 50 removed outlier: 3.787A pdb=" N LEU N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET N 50 " --> pdb=" O HIS N 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 50' Processing helix chain 'N' and resid 73 through 82 removed outlier: 3.555A pdb=" N ILE N 77 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 removed outlier: 4.536A pdb=" N LEU N 109 " --> pdb=" O ASN N 105 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE N 110 " --> pdb=" O PHE N 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.610A pdb=" N ILE O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'P' and resid 3 through 15 removed outlier: 3.736A pdb=" N HIS P 7 " --> pdb=" O LEU P 3 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS P 8 " --> pdb=" O LYS P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 108 removed outlier: 3.961A pdb=" N LEU P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 128 removed outlier: 4.033A pdb=" N TYR P 127 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 123 through 128' Processing helix chain 'P' and resid 133 through 141 removed outlier: 4.058A pdb=" N ARG P 139 " --> pdb=" O ASN P 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.885A 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 96 through 98 removed outlier: 6.400A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.135A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.196A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'M' and resid 7 through 8 Processing sheet with id=AB3, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AB4, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AB5, first strand: chain 'O' and resid 13 through 16 removed outlier: 3.584A pdb=" N LEU O 15 " --> pdb=" O ILE O 3 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LEU O 67 " --> pdb=" O GLN O 2 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 41 through 42 removed outlier: 3.603A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 44 through 45 Processing sheet with id=AB8, first strand: chain 'P' and resid 21 through 25 removed outlier: 3.501A pdb=" N SER P 22 " --> pdb=" O THR P 36 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1203 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 128 basepair parallelities 268 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3139 1.33 - 1.45: 4865 1.45 - 1.57: 7649 1.57 - 1.69: 576 1.69 - 1.81: 57 Bond restraints: 16286 Sorted by residual: bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.334 1.376 -0.043 8.40e-03 1.42e+04 2.58e+01 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.367 0.146 3.90e-02 6.57e+02 1.40e+01 bond pdb=" CB GLU E 73 " pdb=" CG GLU E 73 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.82e+00 bond pdb=" CB ARG F 40 " pdb=" CG ARG F 40 " ideal model delta sigma weight residual 1.520 1.442 0.078 3.00e-02 1.11e+03 6.75e+00 bond pdb=" CB THR H 96 " pdb=" CG2 THR H 96 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 16281 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 22651 2.42 - 4.85: 493 4.85 - 7.27: 77 7.27 - 9.69: 12 9.69 - 12.12: 7 Bond angle restraints: 23240 Sorted by residual: angle pdb=" C LYS C 15 " pdb=" N THR C 16 " pdb=" CA THR C 16 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" C LYS G 15 " pdb=" N THR G 16 " pdb=" CA THR G 16 " ideal model delta sigma weight residual 121.54 133.09 -11.55 1.91e+00 2.74e-01 3.66e+01 angle pdb=" CB ARG M 70 " pdb=" CG ARG M 70 " pdb=" CD ARG M 70 " ideal model delta sigma weight residual 111.30 122.60 -11.30 2.30e+00 1.89e-01 2.41e+01 angle pdb=" CA ARG F 39 " pdb=" CB ARG F 39 " pdb=" CG ARG F 39 " ideal model delta sigma weight residual 114.10 105.98 8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" C LYS F 20 " pdb=" N VAL F 21 " pdb=" CA VAL F 21 " ideal model delta sigma weight residual 121.97 129.27 -7.30 1.80e+00 3.09e-01 1.64e+01 ... (remaining 23235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 7860 35.42 - 70.83: 1255 70.83 - 106.25: 1 106.25 - 141.67: 0 141.67 - 177.09: 2 Dihedral angle restraints: 9118 sinusoidal: 5639 harmonic: 3479 Sorted by residual: dihedral pdb=" CA GLY P 48 " pdb=" C GLY P 48 " pdb=" N VAL P 49 " pdb=" CA VAL P 49 " ideal model delta harmonic sigma weight residual 180.00 -134.44 -45.56 0 5.00e+00 4.00e-02 8.30e+01 dihedral pdb=" CA ARG B 39 " pdb=" C ARG B 39 " pdb=" N ARG B 40 " pdb=" CA ARG B 40 " ideal model delta harmonic sigma weight residual 180.00 149.13 30.87 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ILE H 69 " pdb=" C ILE H 69 " pdb=" N PHE H 70 " pdb=" CA PHE H 70 " ideal model delta harmonic sigma weight residual 180.00 149.72 30.28 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 9115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2560 0.123 - 0.246: 78 0.246 - 0.368: 5 0.368 - 0.491: 0 0.491 - 0.614: 1 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE E 62 " pdb=" CA ILE E 62 " pdb=" CG1 ILE E 62 " pdb=" CG2 ILE E 62 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.42e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB THR C 16 " pdb=" CA THR C 16 " pdb=" OG1 THR C 16 " pdb=" CG2 THR C 16 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 2641 not shown) Planarity restraints: 1942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 98 " -0.002 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR F 98 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR F 98 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR F 98 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR F 98 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR F 98 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 98 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 98 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY P 48 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C GLY P 48 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY P 48 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL P 49 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 13 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C LYS C 13 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS C 13 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA C 14 " -0.014 2.00e-02 2.50e+03 ... (remaining 1939 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3654 2.81 - 3.33: 11961 3.33 - 3.86: 27397 3.86 - 4.38: 35337 4.38 - 4.90: 50424 Nonbonded interactions: 128773 Sorted by model distance: nonbonded pdb=" OG SER P 22 " pdb=" OG1 THR P 36 " model vdw 2.289 3.040 nonbonded pdb=" O ILE N 53 " pdb=" NH1 ARG P 5 " model vdw 2.317 3.120 nonbonded pdb=" NH1 ARG D 31 " pdb=" OP1 DG J 51 " model vdw 2.333 3.120 nonbonded pdb=" OH TYR M 80 " pdb=" OE1 GLU M 90 " model vdw 2.338 3.040 nonbonded pdb=" NH2 ARG G 29 " pdb=" OP1 DC I 49 " model vdw 2.349 3.120 ... (remaining 128768 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 31 through 125) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.480 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.410 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.009 0.146 16286 Z= 0.533 Angle : 0.934 12.117 23240 Z= 0.517 Chirality : 0.056 0.614 2644 Planarity : 0.006 0.057 1942 Dihedral : 23.197 177.086 6866 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.29 % Allowed : 1.27 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.17), residues: 1171 helix: -4.45 (0.09), residues: 631 sheet: -1.78 (0.72), residues: 53 loop : -2.25 (0.23), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP P 33 HIS 0.011 0.003 HIS E 113 PHE 0.041 0.005 PHE F 61 TYR 0.048 0.004 TYR F 98 ARG 0.013 0.002 ARG P 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 367 time to evaluate : 1.301 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 106 ASP cc_start: 0.8164 (m-30) cc_final: 0.7757 (m-30) REVERT: D 63 ASN cc_start: 0.7781 (m-40) cc_final: 0.7540 (m110) REVERT: E 58 THR cc_start: 0.8968 (p) cc_final: 0.8754 (p) REVERT: N 22 TYR cc_start: 0.7669 (t80) cc_final: 0.7377 (t80) outliers start: 3 outliers final: 0 residues processed: 369 average time/residue: 0.4815 time to fit residues: 227.2686 Evaluate side-chains 266 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 82 HIS C 112 GLN D 47 GLN D 82 HIS E 76 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS G 94 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS M 76 GLN O 25 ASN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN P 79 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16286 Z= 0.259 Angle : 0.661 6.984 23240 Z= 0.380 Chirality : 0.042 0.334 2644 Planarity : 0.006 0.043 1942 Dihedral : 28.729 170.453 4475 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.84 % Allowed : 10.37 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.20), residues: 1171 helix: -2.22 (0.16), residues: 650 sheet: -1.01 (0.68), residues: 68 loop : -1.91 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 33 HIS 0.011 0.002 HIS P 32 PHE 0.031 0.002 PHE P 50 TYR 0.016 0.002 TYR H 42 ARG 0.010 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 305 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7950 (tptt) REVERT: C 56 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6993 (tt0) REVERT: E 53 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7498 (ttm110) REVERT: E 58 THR cc_start: 0.9143 (p) cc_final: 0.8926 (p) outliers start: 29 outliers final: 16 residues processed: 318 average time/residue: 0.3807 time to fit residues: 160.9703 Evaluate side-chains 282 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 266 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 64 ARG Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 138 optimal weight: 0.0870 chunk 114 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS D 47 GLN D 63 ASN D 82 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS M 76 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16286 Z= 0.232 Angle : 0.594 6.811 23240 Z= 0.345 Chirality : 0.039 0.267 2644 Planarity : 0.004 0.037 1942 Dihedral : 28.544 167.980 4475 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.03 % Allowed : 11.94 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.23), residues: 1171 helix: -0.75 (0.20), residues: 645 sheet: -0.98 (0.73), residues: 58 loop : -1.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 33 HIS 0.008 0.001 HIS P 75 PHE 0.032 0.002 PHE P 50 TYR 0.015 0.001 TYR N 22 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6895 (mt-10) REVERT: B 25 ASN cc_start: 0.8042 (m-40) cc_final: 0.7662 (m110) REVERT: C 24 GLN cc_start: 0.7582 (mt0) cc_final: 0.7071 (mt0) outliers start: 31 outliers final: 18 residues processed: 295 average time/residue: 0.3655 time to fit residues: 144.7862 Evaluate side-chains 272 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 254 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 ASN D 82 HIS E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16286 Z= 0.289 Angle : 0.612 10.306 23240 Z= 0.353 Chirality : 0.041 0.313 2644 Planarity : 0.005 0.036 1942 Dihedral : 28.701 166.033 4475 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.23 % Allowed : 13.60 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1171 helix: -0.04 (0.21), residues: 648 sheet: -0.66 (0.74), residues: 58 loop : -1.39 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 33 HIS 0.008 0.001 HIS P 75 PHE 0.031 0.002 PHE P 50 TYR 0.017 0.002 TYR N 22 ARG 0.007 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 279 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8715 (t80) cc_final: 0.8466 (t80) REVERT: E 53 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7824 (ttp-110) REVERT: N 16 THR cc_start: 0.8318 (t) cc_final: 0.7230 (p) outliers start: 33 outliers final: 21 residues processed: 296 average time/residue: 0.3744 time to fit residues: 147.7663 Evaluate side-chains 296 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 275 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 73 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 82 HIS E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16286 Z= 0.277 Angle : 0.599 7.287 23240 Z= 0.346 Chirality : 0.040 0.300 2644 Planarity : 0.004 0.042 1942 Dihedral : 28.651 167.412 4475 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.91 % Allowed : 13.41 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1171 helix: 0.43 (0.21), residues: 647 sheet: -0.45 (0.75), residues: 58 loop : -1.27 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 17 HIS 0.008 0.001 HIS P 75 PHE 0.032 0.002 PHE P 50 TYR 0.021 0.002 TYR M 46 ARG 0.006 0.001 ARG N 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6667 (mt0) REVERT: C 50 TYR cc_start: 0.8770 (t80) cc_final: 0.8530 (t80) REVERT: D 59 MET cc_start: 0.8061 (tpt) cc_final: 0.7825 (tpt) REVERT: E 53 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7850 (ttp-110) outliers start: 40 outliers final: 24 residues processed: 299 average time/residue: 0.3807 time to fit residues: 152.5300 Evaluate side-chains 288 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 99 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.0030 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 0.0270 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 GLN ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16286 Z= 0.178 Angle : 0.579 7.444 23240 Z= 0.337 Chirality : 0.038 0.283 2644 Planarity : 0.004 0.038 1942 Dihedral : 28.548 168.305 4475 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.23 % Allowed : 15.36 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1171 helix: 0.68 (0.21), residues: 653 sheet: -0.36 (0.75), residues: 58 loop : -1.16 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 17 HIS 0.007 0.001 HIS P 75 PHE 0.031 0.001 PHE P 50 TYR 0.038 0.002 TYR G 57 ARG 0.008 0.001 ARG P 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 271 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8707 (t80) cc_final: 0.8505 (t80) REVERT: D 59 MET cc_start: 0.8063 (tpt) cc_final: 0.7315 (tpt) REVERT: E 53 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7806 (ttp-110) outliers start: 33 outliers final: 23 residues processed: 286 average time/residue: 0.3600 time to fit residues: 137.8881 Evaluate side-chains 285 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 84 ASN M 76 GLN ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN P 79 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 16286 Z= 0.426 Angle : 0.679 7.797 23240 Z= 0.385 Chirality : 0.046 0.423 2644 Planarity : 0.005 0.045 1942 Dihedral : 29.026 167.860 4475 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.72 % Allowed : 14.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1171 helix: 0.61 (0.21), residues: 652 sheet: -0.63 (0.73), residues: 58 loop : -1.32 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 141 HIS 0.008 0.002 HIS P 75 PHE 0.028 0.002 PHE P 50 TYR 0.023 0.002 TYR G 57 ARG 0.009 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8845 (t80) cc_final: 0.8606 (t80) REVERT: D 59 MET cc_start: 0.8045 (tpt) cc_final: 0.7400 (tpt) REVERT: D 121 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: E 53 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7726 (ttm110) REVERT: G 95 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8066 (mtpp) REVERT: M 46 TYR cc_start: 0.8631 (t80) cc_final: 0.8422 (t80) outliers start: 38 outliers final: 27 residues processed: 278 average time/residue: 0.3782 time to fit residues: 139.5334 Evaluate side-chains 285 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 49 VAL Chi-restraints excluded: chain P residue 99 ILE Chi-restraints excluded: chain P residue 147 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16286 Z= 0.206 Angle : 0.603 8.578 23240 Z= 0.350 Chirality : 0.040 0.366 2644 Planarity : 0.004 0.043 1942 Dihedral : 28.863 169.634 4475 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.74 % Allowed : 15.75 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1171 helix: 0.90 (0.21), residues: 649 sheet: -0.53 (0.74), residues: 58 loop : -1.18 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 17 HIS 0.007 0.001 HIS P 75 PHE 0.037 0.002 PHE P 50 TYR 0.016 0.001 TYR G 57 ARG 0.009 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 261 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8801 (t80) cc_final: 0.8573 (t80) REVERT: D 59 MET cc_start: 0.8083 (tpt) cc_final: 0.7874 (tpt) REVERT: D 121 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6434 (m-80) REVERT: E 53 ARG cc_start: 0.8101 (ttm-80) cc_final: 0.7719 (ttm110) outliers start: 28 outliers final: 24 residues processed: 278 average time/residue: 0.3849 time to fit residues: 142.3712 Evaluate side-chains 284 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 259 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 121 TYR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN P 79 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 16286 Z= 0.344 Angle : 0.640 8.977 23240 Z= 0.366 Chirality : 0.043 0.395 2644 Planarity : 0.005 0.038 1942 Dihedral : 28.899 170.454 4475 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.84 % Allowed : 16.14 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1171 helix: 0.90 (0.21), residues: 654 sheet: -0.72 (0.71), residues: 58 loop : -1.31 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 93 HIS 0.008 0.001 HIS P 75 PHE 0.033 0.002 PHE P 50 TYR 0.022 0.002 TYR G 57 ARG 0.008 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8832 (t80) cc_final: 0.8605 (t80) REVERT: E 53 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7750 (ttm110) REVERT: F 35 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7389 (mtp85) outliers start: 29 outliers final: 23 residues processed: 275 average time/residue: 0.3832 time to fit residues: 139.5155 Evaluate side-chains 276 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 79 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 119 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 16286 Z= 0.304 Angle : 0.631 9.468 23240 Z= 0.361 Chirality : 0.042 0.404 2644 Planarity : 0.005 0.051 1942 Dihedral : 28.863 171.580 4475 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.45 % Allowed : 16.83 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1171 helix: 1.02 (0.21), residues: 652 sheet: -0.81 (0.70), residues: 58 loop : -1.23 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 33 HIS 0.007 0.001 HIS P 75 PHE 0.046 0.002 PHE P 50 TYR 0.020 0.002 TYR G 57 ARG 0.008 0.001 ARG A 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 261 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TYR cc_start: 0.8815 (t80) cc_final: 0.8594 (t80) REVERT: E 53 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7753 (ttm110) REVERT: F 35 ARG cc_start: 0.7912 (mtp85) cc_final: 0.7423 (mtp85) REVERT: N 84 ASN cc_start: 0.8293 (p0) cc_final: 0.7938 (p0) REVERT: P 30 MET cc_start: 0.7433 (mmm) cc_final: 0.7128 (mmt) REVERT: P 127 TYR cc_start: 0.3938 (m-80) cc_final: 0.3606 (m-80) outliers start: 25 outliers final: 23 residues processed: 277 average time/residue: 0.3786 time to fit residues: 138.8972 Evaluate side-chains 279 residues out of total 1031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain M residue 69 ILE Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 67 CYS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 81 ARG Chi-restraints excluded: chain P residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 HIS ** P 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092662 restraints weight = 21912.794| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.77 r_work: 0.2895 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16286 Z= 0.183 Angle : 0.602 9.447 23240 Z= 0.349 Chirality : 0.039 0.349 2644 Planarity : 0.004 0.047 1942 Dihedral : 28.826 172.168 4475 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.66 % Allowed : 17.61 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1171 helix: 1.19 (0.21), residues: 652 sheet: -0.82 (0.70), residues: 58 loop : -1.18 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 93 HIS 0.008 0.001 HIS P 75 PHE 0.059 0.002 PHE E 67 TYR 0.017 0.001 TYR G 57 ARG 0.009 0.001 ARG A 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3891.17 seconds wall clock time: 69 minutes 11.96 seconds (4151.96 seconds total)