Starting phenix.real_space_refine on Mon Mar 11 18:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmv_4083/03_2024/5lmv_4083_neut_updated.pdb" } resolution = 4.9 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= 0.001 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1610 5.49 5 Mg 2 5.21 5 S 74 5.16 5 C 31047 2.51 5 N 11169 2.21 5 O 15566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 128": "NH1" <-> "NH2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 76": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "W GLU 15": "OE1" <-> "OE2" Residue "W GLU 31": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Residue "a GLU 58": "OE1" <-> "OE2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "a GLU 190": "OE1" <-> "OE2" Residue "a GLU 204": "OE1" <-> "OE2" Residue "a GLU 235": "OE1" <-> "OE2" Residue "a GLU 237": "OE1" <-> "OE2" Residue "a ARG 240": "NH1" <-> "NH2" Residue "a GLU 246": "OE1" <-> "OE2" Residue "a ARG 248": "NH1" <-> "NH2" Residue "a GLU 315": "OE1" <-> "OE2" Residue "a GLU 330": "OE1" <-> "OE2" Residue "a GLU 341": "OE1" <-> "OE2" Residue "a GLU 349": "OE1" <-> "OE2" Residue "a GLU 350": "OE1" <-> "OE2" Residue "a GLU 444": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59470 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 32548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32548 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "'] Classifications: {'RNA': 1515} Modifications used: {'5*END': 2, 'rna2p_pur': 107, 'rna2p_pyr': 74, 'rna3p_pur': 748, 'rna3p_pyr': 586} Link IDs: {'rna2p': 181, 'rna3p': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "S" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 655 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} 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: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "W" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "X" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1336 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "Z" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 12, 'rna3p': 64} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3774 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 21, 'TRANS': 480} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 2 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36119 SG CYS D 9 85.646 107.539 147.467 1.00 50.00 S ATOM 36262 SG CYS D 26 82.688 108.924 147.585 1.00 50.00 S ATOM 36302 SG CYS D 31 84.937 110.726 146.868 1.00 50.00 S ATOM 46910 SG CYS N 24 148.306 117.606 137.900 1.00 50.00 S ATOM 46934 SG CYS N 27 146.414 115.305 136.441 1.00 50.00 S ATOM 47041 SG CYS N 40 147.984 116.975 134.239 1.00 50.00 S ATOM 47066 SG CYS N 43 145.025 118.599 135.656 1.00 50.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN N 101 " occ=0.92 residue: pdb="MG MG W 101 " occ=0.63 Time building chain proxies: 23.62, per 1000 atoms: 0.40 Number of scatterers: 59470 At special positions: 0 Unit cell: (225.12, 184.92, 209.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 74 16.00 P 1610 15.00 Mg 2 11.99 O 15566 8.00 N 11169 7.00 C 31047 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 - 3.50 Amino acid : False - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 27.32 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " Number of angles added : 6 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 31 sheets defined 33.3% alpha, 16.4% beta 513 base pairs and 939 stacking pairs defined. Time for finding SS restraints: 27.73 Creating SS restraints... Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 75 through 87 removed outlier: 4.632A pdb=" N ASP B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 Processing helix chain 'B' and resid 132 through 151 removed outlier: 6.103A pdb=" N ARG B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 68 removed outlier: 3.638A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 91 through 98 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.910A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 16 through 32 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.788A pdb=" N ASN F 73 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 103 through 106 removed outlier: 3.658A pdb=" N GLY H 106 " --> pdb=" O VAL H 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 106' Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.774A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 92 through 95 Processing helix chain 'J' and resid 13 through 30 Processing helix chain 'J' and resid 81 through 87 removed outlier: 4.841A pdb=" N MET J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 75 Processing helix chain 'K' and resid 89 through 101 removed outlier: 4.691A pdb=" N GLU K 92 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN K 93 " --> pdb=" O GLY K 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 117 through 120 No H-bonds generated for 'chain 'L' and resid 117 through 120' Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.593A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 37 Processing helix chain 'M' and resid 50 through 63 Processing helix chain 'M' and resid 68 through 83 Processing helix chain 'M' and resid 87 through 94 Processing helix chain 'M' and resid 108 through 111 No H-bonds generated for 'chain 'M' and resid 108 through 111' Processing helix chain 'N' and resid 41 through 50 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 51 through 73 Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 77 Processing helix chain 'Q' and resid 83 through 97 removed outlier: 3.520A pdb=" N SER Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 37 through 40 No H-bonds generated for 'chain 'R' and resid 37 through 40' Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 16 through 21 removed outlier: 3.720A pdb=" N LEU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU S 21 " --> pdb=" O GLU S 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 16 through 21' Processing helix chain 'S' and resid 64 through 68 removed outlier: 3.634A pdb=" N VAL S 67 " --> pdb=" O GLU S 64 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY S 68 " --> pdb=" O ASN S 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 64 through 68' Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'T' and resid 13 through 46 removed outlier: 4.023A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 76 through 93 Processing helix chain 'V' and resid 9 through 15 Processing helix chain 'W' and resid 38 through 43 Processing helix chain 'X' and resid 31 through 41 Processing helix chain 'X' and resid 62 through 77 Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 129 through 143 Processing helix chain 'a' and resid 62 through 65 No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 86 through 98 removed outlier: 3.774A pdb=" N ILE a 98 " --> pdb=" O ARG a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 171 Processing helix chain 'a' and resid 189 through 199 Processing helix chain 'a' and resid 223 through 237 Processing helix chain 'a' and resid 329 through 352 removed outlier: 3.753A pdb=" N ARG a 346 " --> pdb=" O GLU a 342 " (cutoff:3.500A) Processing helix chain 'a' and resid 361 through 366 Processing helix chain 'a' and resid 382 through 394 removed outlier: 3.821A pdb=" N GLU a 386 " --> pdb=" O GLN a 382 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA a 387 " --> pdb=" O GLY a 383 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG a 394 " --> pdb=" O HIS a 390 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 423 Processing helix chain 'a' and resid 436 through 445 Processing helix chain 'a' and resid 455 through 464 Processing sheet with id= A, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.567A pdb=" N ALA B 161 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL B 71 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE B 163 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL B 164 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 185 " --> pdb=" O VAL B 164 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.371A pdb=" N ALA C 100 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL C 68 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN C 102 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL C 70 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLN C 104 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 164 through 171 removed outlier: 3.544A pdb=" N SER C 154 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= E, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= F, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.779A pdb=" N GLY E 44 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 32 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 80 through 84 Processing sheet with id= H, first strand: chain 'F' and resid 44 through 47 removed outlier: 3.577A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 73 through 80 Processing sheet with id= J, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= K, first strand: chain 'H' and resid 82 through 85 removed outlier: 6.804A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 3 through 6 Processing sheet with id= M, first strand: chain 'J' and resid 68 through 74 removed outlier: 3.734A pdb=" N VAL J 72 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 43 through 48 Processing sheet with id= O, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.632A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG K 85 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 81 through 85 removed outlier: 3.916A pdb=" N SER L 81 " --> pdb=" O CYS L 37 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS L 54 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG L 97 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N TYR L 69 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS L 99 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.773A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 71 through 73 removed outlier: 14.804A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Q' and resid 55 through 58 removed outlier: 6.072A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= U, first strand: chain 'W' and resid 52 through 57 removed outlier: 6.741A pdb=" N ARG W 23 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ALA W 16 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR W 21 " --> pdb=" O ALA W 16 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'W' and resid 33 through 36 Processing sheet with id= W, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.857A pdb=" N VAL X 19 " --> pdb=" O PRO X 55 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA X 57 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY X 49 " --> pdb=" O VAL X 56 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'X' and resid 85 through 90 removed outlier: 6.632A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET X 152 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 76 through 78 removed outlier: 7.401A pdb=" N ILE a 146 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE a 176 " --> pdb=" O ILE a 149 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE a 151 " --> pdb=" O ILE a 176 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA a 178 " --> pdb=" O ILE a 151 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE a 211 " --> pdb=" O PHE a 177 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE a 179 " --> pdb=" O ILE a 211 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE a 213 " --> pdb=" O ILE a 179 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'a' and resid 113 through 116 Processing sheet with id= AA, first strand: chain 'a' and resid 284 through 287 removed outlier: 3.665A pdb=" N ALA a 284 " --> pdb=" O ALA a 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL a 280 " --> pdb=" O GLU a 324 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL a 250 " --> pdb=" O VAL a 268 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL a 268 " --> pdb=" O VAL a 250 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'a' and resid 253 through 256 removed outlier: 3.715A pdb=" N GLU a 253 " --> pdb=" O ASN a 265 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'a' and resid 401 through 404 removed outlier: 3.535A pdb=" N ALA a 426 " --> pdb=" O ASN a 374 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU a 448 " --> pdb=" O ILE a 427 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA a 429 " --> pdb=" O LEU a 448 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS a 450 " --> pdb=" O ALA a 429 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'a' and resid 377 through 379 removed outlier: 3.552A pdb=" N GLN a 408 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA a 379 " --> pdb=" O GLN a 408 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'a' and resid 520 through 525 removed outlier: 6.906A pdb=" N VAL a 514 " --> pdb=" O ILE a 521 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN a 523 " --> pdb=" O VAL a 512 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL a 512 " --> pdb=" O GLN a 523 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU a 511 " --> pdb=" O PHE a 564 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY a 498 " --> pdb=" O ARG a 485 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2631 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1379 hydrogen bonds 2386 hydrogen bond angles 0 basepair planarities 513 basepair parallelities 939 stacking parallelities Total time for adding SS restraints: 45.91 Time building geometry restraints manager: 29.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11814 1.34 - 1.46: 22823 1.46 - 1.58: 25994 1.58 - 1.70: 3212 1.70 - 1.82: 131 Bond restraints: 63974 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.358 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.405 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.340 -0.158 2.00e-02 2.50e+03 6.23e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.344 0.154 2.00e-02 2.50e+03 5.92e+01 ... (remaining 63969 not shown) Histogram of bond angle deviations from ideal: 75.81 - 88.26: 4 88.26 - 100.71: 61 100.71 - 113.16: 43584 113.16 - 125.61: 44366 125.61 - 138.07: 6323 Bond angle restraints: 94338 Sorted by residual: angle pdb=" C THR I 7 " pdb=" CA THR I 7 " pdb=" CB THR I 7 " ideal model delta sigma weight residual 111.23 75.81 35.42 1.68e+00 3.54e-01 4.45e+02 angle pdb=" N ARG E 15 " pdb=" CA ARG E 15 " pdb=" C ARG E 15 " ideal model delta sigma weight residual 110.20 77.04 33.16 1.58e+00 4.01e-01 4.40e+02 angle pdb=" N ARG W 23 " pdb=" CA ARG W 23 " pdb=" C ARG W 23 " ideal model delta sigma weight residual 110.28 83.72 26.56 1.48e+00 4.57e-01 3.22e+02 angle pdb=" C ALA K 89 " pdb=" CA ALA K 89 " pdb=" CB ALA K 89 " ideal model delta sigma weight residual 110.42 138.07 -27.65 1.99e+00 2.53e-01 1.93e+02 angle pdb=" C LEU W 33 " pdb=" CA LEU W 33 " pdb=" CB LEU W 33 " ideal model delta sigma weight residual 110.16 87.30 22.86 1.66e+00 3.63e-01 1.90e+02 ... (remaining 94333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 35556 35.85 - 71.70: 4982 71.70 - 107.55: 632 107.55 - 143.40: 27 143.40 - 179.25: 47 Dihedral angle restraints: 41244 sinusoidal: 32296 harmonic: 8948 Sorted by residual: dihedral pdb=" C ALA K 89 " pdb=" N ALA K 89 " pdb=" CA ALA K 89 " pdb=" CB ALA K 89 " ideal model delta harmonic sigma weight residual -122.60 -169.07 46.47 0 2.50e+00 1.60e-01 3.46e+02 dihedral pdb=" N ALA K 89 " pdb=" C ALA K 89 " pdb=" CA ALA K 89 " pdb=" CB ALA K 89 " ideal model delta harmonic sigma weight residual 122.90 164.62 -41.72 0 2.50e+00 1.60e-01 2.79e+02 dihedral pdb=" C THR I 7 " pdb=" N THR I 7 " pdb=" CA THR I 7 " pdb=" CB THR I 7 " ideal model delta harmonic sigma weight residual -122.00 -82.63 -39.37 0 2.50e+00 1.60e-01 2.48e+02 ... (remaining 41241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 11708 0.383 - 0.767: 54 0.767 - 1.150: 4 1.150 - 1.534: 0 1.534 - 1.917: 1 Chirality restraints: 11767 Sorted by residual: chirality pdb=" CA ALA K 89 " pdb=" N ALA K 89 " pdb=" C ALA K 89 " pdb=" CB ALA K 89 " both_signs ideal model delta sigma weight residual False 2.48 0.57 1.92 2.00e-01 2.50e+01 9.19e+01 chirality pdb=" C3' G A 181 " pdb=" C4' G A 181 " pdb=" O3' G A 181 " pdb=" C2' G A 181 " both_signs ideal model delta sigma weight residual False -2.74 -1.87 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C3' A A 792 " pdb=" C4' A A 792 " pdb=" O3' A A 792 " pdb=" C2' A A 792 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.82 2.00e-01 2.50e+01 1.69e+01 ... (remaining 11764 not shown) Planarity restraints: 6019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC Z 32 " 0.051 2.00e-02 2.50e+03 5.10e-01 5.85e+03 pdb=" C4' OMC Z 32 " -0.411 2.00e-02 2.50e+03 pdb=" O4' OMC Z 32 " -0.589 2.00e-02 2.50e+03 pdb=" C3' OMC Z 32 " 0.576 2.00e-02 2.50e+03 pdb=" O3' OMC Z 32 " 0.413 2.00e-02 2.50e+03 pdb=" C2' OMC Z 32 " 0.249 2.00e-02 2.50e+03 pdb=" O2' OMC Z 32 " -0.785 2.00e-02 2.50e+03 pdb=" C1' OMC Z 32 " -0.263 2.00e-02 2.50e+03 pdb=" N1 OMC Z 32 " 0.758 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4SU Z 8 " -0.294 2.00e-02 2.50e+03 4.35e-01 4.26e+03 pdb=" C4' 4SU Z 8 " 0.402 2.00e-02 2.50e+03 pdb=" O4' 4SU Z 8 " 0.698 2.00e-02 2.50e+03 pdb=" C3' 4SU Z 8 " -0.483 2.00e-02 2.50e+03 pdb=" O3' 4SU Z 8 " -0.070 2.00e-02 2.50e+03 pdb=" C2' 4SU Z 8 " -0.380 2.00e-02 2.50e+03 pdb=" O2' 4SU Z 8 " 0.416 2.00e-02 2.50e+03 pdb=" C1' 4SU Z 8 " 0.287 2.00e-02 2.50e+03 pdb=" N1 4SU Z 8 " -0.576 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' G7M Z 46 " 0.015 2.00e-02 2.50e+03 4.01e-01 3.63e+03 pdb=" C4' G7M Z 46 " -0.391 2.00e-02 2.50e+03 pdb=" O4' G7M Z 46 " -0.321 2.00e-02 2.50e+03 pdb=" C3' G7M Z 46 " 0.520 2.00e-02 2.50e+03 pdb=" O3' G7M Z 46 " 0.274 2.00e-02 2.50e+03 pdb=" C2' G7M Z 46 " 0.300 2.00e-02 2.50e+03 pdb=" O2' G7M Z 46 " -0.660 2.00e-02 2.50e+03 pdb=" C1' G7M Z 46 " -0.249 2.00e-02 2.50e+03 pdb=" N9 G7M Z 46 " 0.512 2.00e-02 2.50e+03 ... (remaining 6016 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.76: 3 1.76 - 2.55: 187 2.55 - 3.33: 67091 3.33 - 4.12: 198123 4.12 - 4.90: 278755 Warning: very small nonbonded interaction distances. Nonbonded interactions: 544159 Sorted by model distance: nonbonded pdb=" CG2 ILE J 38 " pdb=" O LEU J 71 " model vdw 0.977 3.460 nonbonded pdb=" OP2 A A 439 " pdb=" N2 G A 493 " model vdw 1.414 2.520 nonbonded pdb=" OP2 A Z 73 " pdb=" OG1 THR a 492 " model vdw 1.735 2.440 nonbonded pdb=" O4 U A1358 " pdb=" N1 A A1363A" model vdw 1.769 2.496 nonbonded pdb=" O ALA D 32 " pdb=" O ARG D 36 " model vdw 1.843 3.040 ... (remaining 544154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.63 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.060 Extract box with map and model: 6.330 Check model and map are aligned: 0.680 Set scattering table: 0.440 Process input model: 178.480 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 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 : 0.008 0.312 63974 Z= 0.469 Angle : 1.336 35.424 94338 Z= 0.894 Chirality : 0.113 1.917 11767 Planarity : 0.014 0.510 6019 Dihedral : 25.944 179.250 35490 Min Nonbonded Distance : 0.977 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 2.51 % Allowed : 9.64 % Favored : 87.85 % Rotamer: Outliers : 15.18 % Allowed : 18.05 % Favored : 66.77 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3071 helix: 0.76 (0.12), residues: 1129 sheet: -1.48 (0.20), residues: 534 loop : -3.10 (0.13), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 138 HIS 0.012 0.002 HIS D 43 PHE 0.023 0.003 PHE D 93 TYR 0.025 0.002 TYR O 78 ARG 0.024 0.002 ARG D 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1557 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1167 time to evaluate : 3.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6390 (pptt) REVERT: B 41 ILE cc_start: 0.2227 (OUTLIER) cc_final: 0.1457 (pt) REVERT: B 61 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7420 (pp) REVERT: B 206 ASP cc_start: 0.2585 (OUTLIER) cc_final: 0.2345 (t0) REVERT: C 47 LEU cc_start: 0.8312 (mp) cc_final: 0.8060 (mt) REVERT: C 94 LEU cc_start: 0.7785 (tt) cc_final: 0.7555 (tt) REVERT: C 101 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5021 (mm) REVERT: C 151 VAL cc_start: 0.7151 (t) cc_final: 0.6928 (t) REVERT: C 203 PHE cc_start: 0.4359 (t80) cc_final: 0.3879 (t80) REVERT: D 39 PRO cc_start: 0.6588 (Cg_endo) cc_final: 0.6307 (Cg_endo) REVERT: D 58 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7529 (tm) REVERT: D 102 ASP cc_start: 0.5597 (p0) cc_final: 0.4681 (p0) REVERT: D 161 ASN cc_start: 0.6743 (m-40) cc_final: 0.5922 (m110) REVERT: D 173 TRP cc_start: 0.6216 (p90) cc_final: 0.5428 (p90) REVERT: E 41 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6585 (m) REVERT: E 110 LEU cc_start: 0.8508 (mt) cc_final: 0.8174 (mt) REVERT: E 142 LEU cc_start: 0.4711 (OUTLIER) cc_final: 0.3866 (mt) REVERT: E 152 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.4673 (ptt180) REVERT: F 8 ILE cc_start: 0.7176 (mp) cc_final: 0.6959 (mp) REVERT: F 9 VAL cc_start: 0.8521 (t) cc_final: 0.8105 (t) REVERT: F 18 GLN cc_start: 0.5978 (OUTLIER) cc_final: 0.5390 (mp-120) REVERT: F 19 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7606 (tt) REVERT: F 22 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7758 (mm-30) REVERT: F 33 TYR cc_start: 0.7090 (m-80) cc_final: 0.6568 (m-80) REVERT: F 45 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7744 (mt) REVERT: G 26 PHE cc_start: 0.6815 (t80) cc_final: 0.6564 (t80) REVERT: H 27 PRO cc_start: 0.7573 (Cg_exo) cc_final: 0.7118 (Cg_endo) REVERT: H 33 GLU cc_start: 0.8539 (tt0) cc_final: 0.8270 (mt-10) REVERT: H 36 LEU cc_start: 0.8765 (mt) cc_final: 0.8410 (mt) REVERT: H 51 VAL cc_start: 0.7190 (m) cc_final: 0.6913 (p) REVERT: H 107 LEU cc_start: 0.5300 (mt) cc_final: 0.4421 (mt) REVERT: I 3 GLN cc_start: 0.5411 (tt0) cc_final: 0.5193 (pm20) REVERT: I 108 VAL cc_start: 0.6080 (p) cc_final: 0.5851 (p) REVERT: K 48 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6444 (mp) REVERT: K 66 LEU cc_start: 0.8145 (mt) cc_final: 0.7825 (mt) REVERT: L 67 THR cc_start: 0.6837 (p) cc_final: 0.6549 (p) REVERT: M 16 ASP cc_start: 0.7933 (p0) cc_final: 0.7720 (p0) REVERT: M 25 ILE cc_start: 0.4852 (mt) cc_final: 0.4498 (mt) REVERT: M 114 ARG cc_start: 0.3887 (mtt-85) cc_final: 0.2685 (mpt180) REVERT: O 12 ILE cc_start: 0.7916 (mt) cc_final: 0.7651 (mt) REVERT: O 13 GLN cc_start: 0.8654 (mt0) cc_final: 0.8177 (tp40) REVERT: O 43 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (tt) REVERT: O 77 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7086 (mtm180) REVERT: P 23 ASP cc_start: 0.7189 (t70) cc_final: 0.6886 (t70) REVERT: P 44 THR cc_start: 0.2040 (OUTLIER) cc_final: 0.1792 (m) REVERT: P 49 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7448 (pp) REVERT: Q 84 LEU cc_start: 0.9063 (tp) cc_final: 0.8836 (mp) REVERT: Q 91 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7746 (ttt180) REVERT: S 7 LYS cc_start: 0.5246 (OUTLIER) cc_final: 0.4844 (mmtm) REVERT: S 51 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.6458 (m) REVERT: S 77 THR cc_start: 0.3302 (OUTLIER) cc_final: 0.1739 (t) REVERT: T 36 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8125 (tp) REVERT: W 46 ARG cc_start: 0.3137 (OUTLIER) cc_final: 0.1818 (mmp-170) REVERT: W 55 VAL cc_start: 0.8289 (t) cc_final: 0.8078 (t) REVERT: X 32 ARG cc_start: 0.5199 (OUTLIER) cc_final: 0.4782 (mmp80) REVERT: X 164 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7568 (tt) REVERT: a 79 MET cc_start: 0.3410 (ptt) cc_final: 0.3115 (ttt) REVERT: a 154 ASP cc_start: 0.5873 (OUTLIER) cc_final: 0.5579 (p0) REVERT: a 167 HIS cc_start: 0.5206 (OUTLIER) cc_final: 0.4194 (m-70) REVERT: a 197 MET cc_start: 0.7291 (mtm) cc_final: 0.6927 (mtt) REVERT: a 202 VAL cc_start: 0.6238 (t) cc_final: 0.5872 (t) REVERT: a 225 ASP cc_start: 0.7783 (m-30) cc_final: 0.7540 (m-30) outliers start: 390 outliers final: 79 residues processed: 1361 average time/residue: 0.7399 time to fit residues: 1534.1989 Evaluate side-chains 758 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 653 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 389 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 235 optimal weight: 50.0000 chunk 186 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 219 optimal weight: 5.9990 chunk 268 optimal weight: 30.0000 chunk 418 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 95 GLN B 212 GLN C 31 HIS C 98 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 123 HIS D 129 ASN D 161 ASN D 199 ASN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 73 ASN G 13 GLN G 97 GLN G 122 HIS ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN J 68 HIS J 69 ASN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 75 HIS M 62 ASN O 9 GLN ** R 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN ** T 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 224 GLN a 382 GLN a 495 GLN ** a 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 63974 Z= 0.263 Angle : 0.855 14.603 94338 Z= 0.447 Chirality : 0.046 0.380 11767 Planarity : 0.008 0.122 6019 Dihedral : 25.403 179.560 29119 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.55 % Favored : 92.71 % Rotamer: Outliers : 0.47 % Allowed : 6.26 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.15), residues: 3071 helix: 1.60 (0.15), residues: 1119 sheet: -1.28 (0.20), residues: 580 loop : -2.52 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP H 138 HIS 0.025 0.002 HIS K 116 PHE 0.024 0.003 PHE I 18 TYR 0.035 0.003 TYR E 133 ARG 0.031 0.001 ARG E 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 825 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 LEU cc_start: 0.7545 (mp) cc_final: 0.7340 (mp) REVERT: B 138 LEU cc_start: 0.9085 (mt) cc_final: 0.8851 (mt) REVERT: B 146 GLN cc_start: 0.7185 (mt0) cc_final: 0.6772 (pp30) REVERT: C 14 ILE cc_start: 0.8093 (mt) cc_final: 0.7552 (tp) REVERT: D 58 LEU cc_start: 0.7895 (tt) cc_final: 0.7066 (tt) REVERT: D 68 TYR cc_start: 0.7567 (m-10) cc_final: 0.7022 (m-10) REVERT: D 84 LYS cc_start: 0.7417 (tttt) cc_final: 0.7199 (tttt) REVERT: D 103 ASN cc_start: 0.7280 (t0) cc_final: 0.6101 (t0) REVERT: D 190 ASP cc_start: 0.6648 (m-30) cc_final: 0.6337 (m-30) REVERT: E 12 LEU cc_start: 0.8899 (tp) cc_final: 0.8509 (tt) REVERT: E 25 ARG cc_start: 0.7319 (ttt180) cc_final: 0.6717 (ttm170) REVERT: E 130 ASN cc_start: 0.8072 (t0) cc_final: 0.7736 (t0) REVERT: F 14 LEU cc_start: 0.7631 (mt) cc_final: 0.7408 (mt) REVERT: F 22 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7523 (mm-30) REVERT: F 90 VAL cc_start: 0.8428 (m) cc_final: 0.8132 (m) REVERT: G 125 MET cc_start: 0.7493 (mtm) cc_final: 0.7279 (mtp) REVERT: G 131 LYS cc_start: 0.8668 (ptpt) cc_final: 0.8143 (ptpp) REVERT: H 61 VAL cc_start: 0.8560 (t) cc_final: 0.7987 (m) REVERT: I 33 PHE cc_start: 0.5567 (t80) cc_final: 0.5126 (t80) REVERT: I 54 ASP cc_start: 0.8199 (m-30) cc_final: 0.7988 (m-30) REVERT: I 75 ASP cc_start: 0.8012 (m-30) cc_final: 0.7800 (m-30) REVERT: K 21 ILE cc_start: 0.7606 (tt) cc_final: 0.7326 (mp) REVERT: K 66 LEU cc_start: 0.8329 (mt) cc_final: 0.7921 (mt) REVERT: K 108 ILE cc_start: 0.6985 (mp) cc_final: 0.6734 (mp) REVERT: K 110 ASP cc_start: 0.6759 (t0) cc_final: 0.6533 (t0) REVERT: L 60 LEU cc_start: 0.8839 (tp) cc_final: 0.8570 (tp) REVERT: M 25 ILE cc_start: 0.5470 (mt) cc_final: 0.5073 (mt) REVERT: N 36 PHE cc_start: 0.6614 (t80) cc_final: 0.6258 (t80) REVERT: N 37 PHE cc_start: 0.5133 (m-80) cc_final: 0.3204 (m-80) REVERT: O 13 GLN cc_start: 0.8690 (mt0) cc_final: 0.8265 (tp40) REVERT: O 36 ILE cc_start: 0.8539 (mm) cc_final: 0.8209 (mm) REVERT: Q 91 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8450 (ttt180) REVERT: S 18 LYS cc_start: 0.7813 (mttt) cc_final: 0.7597 (mttt) REVERT: T 36 LEU cc_start: 0.8532 (mm) cc_final: 0.8244 (tp) REVERT: T 83 ARG cc_start: 0.8228 (tpm170) cc_final: 0.7756 (tpp-160) REVERT: T 88 VAL cc_start: 0.8779 (t) cc_final: 0.8277 (p) REVERT: X 90 PHE cc_start: 0.7309 (m-10) cc_final: 0.6510 (m-80) REVERT: a 79 MET cc_start: 0.3169 (ptt) cc_final: 0.2743 (ttt) REVERT: a 278 TYR cc_start: 0.4597 (m-10) cc_final: 0.4339 (m-10) outliers start: 12 outliers final: 3 residues processed: 833 average time/residue: 0.7073 time to fit residues: 914.6702 Evaluate side-chains 584 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 581 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 232 optimal weight: 0.0170 chunk 129 optimal weight: 20.0000 chunk 348 optimal weight: 40.0000 chunk 285 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 419 optimal weight: 7.9990 chunk 453 optimal weight: 6.9990 chunk 373 optimal weight: 20.0000 chunk 415 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 336 optimal weight: 20.0000 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN F 64 GLN F 73 ASN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN H 15 ASN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 HIS ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 265 ASN ** a 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 63974 Z= 0.227 Angle : 0.753 13.154 94338 Z= 0.400 Chirality : 0.041 0.277 11767 Planarity : 0.007 0.118 6019 Dihedral : 25.289 179.499 29119 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.13 % Favored : 92.22 % Rotamer: Outliers : 0.19 % Allowed : 5.29 % Favored : 94.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3071 helix: 0.98 (0.15), residues: 1137 sheet: -1.05 (0.20), residues: 569 loop : -2.30 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 48 HIS 0.018 0.002 HIS K 116 PHE 0.023 0.003 PHE B 55 TYR 0.042 0.002 TYR D 68 ARG 0.021 0.001 ARG J 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 753 time to evaluate : 4.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 VAL cc_start: 0.9084 (t) cc_final: 0.8630 (m) REVERT: B 146 GLN cc_start: 0.7023 (mt0) cc_final: 0.6505 (pp30) REVERT: C 14 ILE cc_start: 0.8148 (mt) cc_final: 0.7787 (tp) REVERT: C 84 ILE cc_start: 0.9290 (tt) cc_final: 0.9010 (pt) REVERT: C 186 PHE cc_start: 0.7059 (t80) cc_final: 0.6640 (t80) REVERT: D 84 LYS cc_start: 0.7458 (tttt) cc_final: 0.7200 (tttt) REVERT: D 103 ASN cc_start: 0.7728 (t0) cc_final: 0.6580 (t0) REVERT: D 173 TRP cc_start: 0.6275 (p90) cc_final: 0.5977 (p90) REVERT: D 190 ASP cc_start: 0.6582 (m-30) cc_final: 0.6364 (m-30) REVERT: D 208 SER cc_start: 0.7252 (m) cc_final: 0.7031 (p) REVERT: E 25 ARG cc_start: 0.7455 (ttt180) cc_final: 0.6792 (ttm170) REVERT: F 33 TYR cc_start: 0.8297 (m-80) cc_final: 0.7894 (m-10) REVERT: G 27 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8586 (pt) REVERT: G 66 VAL cc_start: 0.8839 (t) cc_final: 0.8569 (t) REVERT: G 125 MET cc_start: 0.7779 (mtm) cc_final: 0.7348 (mtp) REVERT: H 1 MET cc_start: 0.2589 (ptm) cc_final: 0.1322 (ptm) REVERT: H 20 TYR cc_start: 0.7827 (m-80) cc_final: 0.7551 (m-10) REVERT: H 61 VAL cc_start: 0.8498 (t) cc_final: 0.8173 (t) REVERT: I 33 PHE cc_start: 0.5712 (t80) cc_final: 0.5206 (t80) REVERT: J 14 LYS cc_start: 0.9075 (pptt) cc_final: 0.8804 (pptt) REVERT: K 21 ILE cc_start: 0.7673 (tt) cc_final: 0.7437 (mp) REVERT: K 66 LEU cc_start: 0.8395 (mt) cc_final: 0.7939 (mt) REVERT: L 60 LEU cc_start: 0.8989 (tp) cc_final: 0.8586 (tp) REVERT: N 58 LYS cc_start: 0.6895 (ptmt) cc_final: 0.6313 (ptmt) REVERT: O 13 GLN cc_start: 0.8628 (mt0) cc_final: 0.8394 (mm110) REVERT: O 29 VAL cc_start: 0.9267 (p) cc_final: 0.8998 (p) REVERT: O 36 ILE cc_start: 0.8453 (mm) cc_final: 0.8106 (mm) REVERT: O 54 ARG cc_start: 0.8280 (tmt170) cc_final: 0.7765 (ttt-90) REVERT: Q 5 VAL cc_start: 0.8027 (t) cc_final: 0.7710 (t) REVERT: Q 60 ILE cc_start: 0.7515 (tp) cc_final: 0.7266 (tp) REVERT: Q 73 VAL cc_start: 0.7979 (t) cc_final: 0.7540 (p) REVERT: Q 89 LEU cc_start: 0.8624 (pp) cc_final: 0.8129 (pp) REVERT: S 15 LEU cc_start: 0.8159 (pt) cc_final: 0.7428 (mm) REVERT: T 73 HIS cc_start: 0.6072 (m90) cc_final: 0.5471 (m90) REVERT: X 90 PHE cc_start: 0.7586 (m-10) cc_final: 0.6874 (m-80) REVERT: a 79 MET cc_start: 0.3737 (ptt) cc_final: 0.3113 (ttt) REVERT: a 465 MET cc_start: -0.0613 (ptt) cc_final: -0.0898 (ptt) outliers start: 5 outliers final: 0 residues processed: 756 average time/residue: 0.7022 time to fit residues: 828.1349 Evaluate side-chains 554 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 553 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 414 optimal weight: 20.0000 chunk 315 optimal weight: 0.7980 chunk 217 optimal weight: 7.9990 chunk 46 optimal weight: 30.0000 chunk 200 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 420 optimal weight: 7.9990 chunk 445 optimal weight: 40.0000 chunk 219 optimal weight: 6.9990 chunk 398 optimal weight: 0.6980 chunk 120 optimal weight: 40.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 GLN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 ASN a 119 GLN a 167 HIS a 265 ASN ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63974 Z= 0.199 Angle : 0.717 13.272 94338 Z= 0.379 Chirality : 0.039 0.355 11767 Planarity : 0.006 0.117 6019 Dihedral : 25.201 179.616 29119 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.15 % Favored : 93.32 % Rotamer: Outliers : 0.16 % Allowed : 5.14 % Favored : 94.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.03 % 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: -1.20 (0.15), residues: 3071 helix: 0.72 (0.15), residues: 1126 sheet: -0.86 (0.21), residues: 562 loop : -2.09 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 97 HIS 0.015 0.002 HIS K 116 PHE 0.023 0.003 PHE B 55 TYR 0.033 0.002 TYR D 68 ARG 0.013 0.001 ARG J 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 700 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 VAL cc_start: 0.9101 (t) cc_final: 0.8610 (m) REVERT: B 146 GLN cc_start: 0.7347 (mt0) cc_final: 0.6887 (pp30) REVERT: C 14 ILE cc_start: 0.8321 (mt) cc_final: 0.7703 (tp) REVERT: C 67 THR cc_start: 0.6508 (m) cc_final: 0.6102 (m) REVERT: D 84 LYS cc_start: 0.7531 (tttt) cc_final: 0.7319 (tttt) REVERT: D 103 ASN cc_start: 0.7675 (t0) cc_final: 0.7369 (t0) REVERT: D 161 ASN cc_start: 0.6307 (m110) cc_final: 0.5947 (m110) REVERT: D 208 SER cc_start: 0.7264 (m) cc_final: 0.7038 (p) REVERT: E 11 ILE cc_start: 0.8584 (pt) cc_final: 0.8128 (pt) REVERT: E 26 PHE cc_start: 0.7658 (m-80) cc_final: 0.7430 (m-80) REVERT: E 53 LEU cc_start: 0.8100 (tp) cc_final: 0.7506 (tp) REVERT: E 129 ILE cc_start: 0.8959 (mp) cc_final: 0.8728 (mp) REVERT: E 130 ASN cc_start: 0.7547 (t0) cc_final: 0.7043 (t0) REVERT: F 33 TYR cc_start: 0.8214 (m-80) cc_final: 0.7651 (m-10) REVERT: G 31 MET cc_start: 0.6196 (ttt) cc_final: 0.5395 (ttt) REVERT: G 66 VAL cc_start: 0.8844 (t) cc_final: 0.8597 (t) REVERT: G 125 MET cc_start: 0.7698 (mtm) cc_final: 0.7224 (mtp) REVERT: H 1 MET cc_start: 0.1699 (ptm) cc_final: 0.0622 (ptm) REVERT: I 33 PHE cc_start: 0.4967 (t80) cc_final: 0.4650 (t80) REVERT: J 14 LYS cc_start: 0.9099 (pptt) cc_final: 0.8729 (pptt) REVERT: K 21 ILE cc_start: 0.7589 (tt) cc_final: 0.7256 (mp) REVERT: K 66 LEU cc_start: 0.8092 (mt) cc_final: 0.7668 (mt) REVERT: K 110 ASP cc_start: 0.6031 (t0) cc_final: 0.5824 (t0) REVERT: L 60 LEU cc_start: 0.8888 (tp) cc_final: 0.8451 (tp) REVERT: L 84 LEU cc_start: 0.7054 (tp) cc_final: 0.6416 (tp) REVERT: N 39 LEU cc_start: 0.6980 (mt) cc_final: 0.6654 (mt) REVERT: O 13 GLN cc_start: 0.8706 (mt0) cc_final: 0.8425 (mm110) REVERT: O 36 ILE cc_start: 0.8508 (mm) cc_final: 0.8147 (mm) REVERT: P 49 LEU cc_start: 0.8653 (tt) cc_final: 0.8415 (tt) REVERT: R 30 ASP cc_start: 0.7953 (t0) cc_final: 0.6576 (t0) REVERT: S 18 LYS cc_start: 0.7761 (mttt) cc_final: 0.7552 (mtpt) REVERT: T 36 LEU cc_start: 0.8599 (mm) cc_final: 0.8288 (tp) REVERT: T 73 HIS cc_start: 0.5834 (m90) cc_final: 0.5300 (m90) REVERT: T 83 ARG cc_start: 0.8290 (tpm170) cc_final: 0.7547 (mmm160) REVERT: W 23 ARG cc_start: 0.6549 (ttt180) cc_final: 0.6190 (ttm170) REVERT: W 67 ILE cc_start: 0.7717 (mt) cc_final: 0.7357 (tp) REVERT: X 22 ASP cc_start: 0.6610 (p0) cc_final: 0.6375 (p0) REVERT: X 90 PHE cc_start: 0.7500 (m-10) cc_final: 0.6944 (m-80) REVERT: X 152 MET cc_start: -0.0180 (tmm) cc_final: -0.0815 (tmm) REVERT: a 79 MET cc_start: 0.3593 (ptt) cc_final: 0.2938 (ttt) REVERT: a 465 MET cc_start: 0.0081 (ptt) cc_final: -0.0689 (ptt) outliers start: 4 outliers final: 2 residues processed: 703 average time/residue: 0.6884 time to fit residues: 760.6459 Evaluate side-chains 510 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 508 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 371 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 331 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 380 optimal weight: 8.9990 chunk 308 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 399 optimal weight: 0.2980 chunk 112 optimal weight: 30.0000 overall best weight: 6.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 63974 Z= 0.247 Angle : 0.766 13.341 94338 Z= 0.401 Chirality : 0.040 0.309 11767 Planarity : 0.007 0.119 6019 Dihedral : 25.324 179.778 29119 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 35.56 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.72 % Favored : 91.79 % Rotamer: Outliers : 0.12 % Allowed : 4.16 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.43 (0.14), residues: 3071 helix: 0.39 (0.15), residues: 1125 sheet: -0.92 (0.21), residues: 547 loop : -2.10 (0.15), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 173 HIS 0.020 0.002 HIS L 75 PHE 0.043 0.003 PHE B 55 TYR 0.029 0.002 TYR I 4 ARG 0.044 0.001 ARG W 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 653 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 146 GLN cc_start: 0.7547 (mt0) cc_final: 0.6914 (pp30) REVERT: C 67 THR cc_start: 0.6463 (m) cc_final: 0.5991 (m) REVERT: D 84 LYS cc_start: 0.7586 (tttt) cc_final: 0.7378 (tttt) REVERT: D 161 ASN cc_start: 0.6875 (m110) cc_final: 0.6398 (m110) REVERT: E 26 PHE cc_start: 0.7434 (m-80) cc_final: 0.7156 (m-80) REVERT: E 66 MET cc_start: 0.6584 (tpt) cc_final: 0.6305 (tpp) REVERT: E 130 ASN cc_start: 0.7505 (t0) cc_final: 0.7227 (t0) REVERT: F 33 TYR cc_start: 0.8515 (m-80) cc_final: 0.7772 (m-10) REVERT: G 66 VAL cc_start: 0.8759 (t) cc_final: 0.8544 (t) REVERT: G 106 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7578 (tp-100) REVERT: G 125 MET cc_start: 0.7900 (mtm) cc_final: 0.7334 (mtp) REVERT: H 1 MET cc_start: 0.2136 (ptm) cc_final: 0.1712 (ptm) REVERT: H 20 TYR cc_start: 0.7936 (m-10) cc_final: 0.7690 (m-10) REVERT: H 61 VAL cc_start: 0.8553 (t) cc_final: 0.8067 (t) REVERT: H 107 LEU cc_start: 0.4752 (mm) cc_final: 0.4545 (mm) REVERT: I 33 PHE cc_start: 0.5990 (t80) cc_final: 0.5649 (t80) REVERT: J 14 LYS cc_start: 0.9247 (pptt) cc_final: 0.8838 (pptt) REVERT: J 44 VAL cc_start: 0.7950 (t) cc_final: 0.7729 (t) REVERT: K 21 ILE cc_start: 0.7519 (tt) cc_final: 0.7318 (mp) REVERT: K 83 ILE cc_start: 0.8316 (mm) cc_final: 0.7943 (mm) REVERT: K 124 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7473 (ttmt) REVERT: L 60 LEU cc_start: 0.8879 (tp) cc_final: 0.8606 (tp) REVERT: L 84 LEU cc_start: 0.6927 (tp) cc_final: 0.5875 (tp) REVERT: L 93 LEU cc_start: 0.8139 (mt) cc_final: 0.7919 (mt) REVERT: N 39 LEU cc_start: 0.7783 (mt) cc_final: 0.7098 (mt) REVERT: O 59 MET cc_start: 0.8761 (mmt) cc_final: 0.8347 (mtp) REVERT: O 70 LEU cc_start: 0.9039 (tp) cc_final: 0.8297 (tp) REVERT: P 49 LEU cc_start: 0.8677 (tt) cc_final: 0.8325 (tt) REVERT: Q 82 MET cc_start: 0.7979 (tpp) cc_final: 0.7498 (tpp) REVERT: Q 85 VAL cc_start: 0.9118 (t) cc_final: 0.8289 (t) REVERT: R 30 ASP cc_start: 0.7122 (t0) cc_final: 0.6285 (t0) REVERT: S 18 LYS cc_start: 0.8071 (mttt) cc_final: 0.7537 (mtpt) REVERT: T 73 HIS cc_start: 0.5882 (m90) cc_final: 0.5272 (m90) REVERT: X 22 ASP cc_start: 0.6952 (p0) cc_final: 0.6694 (p0) REVERT: X 90 PHE cc_start: 0.7443 (m-10) cc_final: 0.6814 (m-80) REVERT: X 152 MET cc_start: -0.0060 (tmm) cc_final: -0.1130 (tmm) REVERT: a 79 MET cc_start: 0.3696 (ptt) cc_final: 0.3306 (ttt) REVERT: a 228 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7817 (mt-10) REVERT: a 465 MET cc_start: 0.0549 (ptt) cc_final: -0.0370 (ptt) outliers start: 3 outliers final: 1 residues processed: 655 average time/residue: 0.6630 time to fit residues: 691.9807 Evaluate side-chains 483 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 482 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 149 optimal weight: 30.0000 chunk 401 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 110 optimal weight: 30.0000 chunk 446 optimal weight: 30.0000 chunk 370 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 147 optimal weight: 20.0000 chunk 234 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 HIS ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 63974 Z= 0.221 Angle : 0.728 13.486 94338 Z= 0.383 Chirality : 0.039 0.331 11767 Planarity : 0.007 0.117 6019 Dihedral : 25.341 179.700 29119 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 32.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.45 % Favored : 93.06 % Rotamer: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.51 (0.14), residues: 3071 helix: 0.28 (0.15), residues: 1123 sheet: -0.98 (0.21), residues: 554 loop : -2.10 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP P 59 HIS 0.018 0.002 HIS K 116 PHE 0.048 0.003 PHE B 55 TYR 0.025 0.002 TYR E 133 ARG 0.017 0.001 ARG I 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 621 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: B 146 GLN cc_start: 0.7530 (mt0) cc_final: 0.6981 (pp30) REVERT: C 56 ASP cc_start: 0.7166 (t0) cc_final: 0.6962 (t0) REVERT: C 67 THR cc_start: 0.6522 (m) cc_final: 0.5633 (m) REVERT: C 186 PHE cc_start: 0.7257 (t80) cc_final: 0.7013 (t80) REVERT: D 57 ARG cc_start: 0.8662 (mpp-170) cc_final: 0.8402 (ptp-170) REVERT: D 66 ARG cc_start: 0.6489 (mpt180) cc_final: 0.6280 (mpt180) REVERT: D 84 LYS cc_start: 0.7648 (tttt) cc_final: 0.7406 (tttt) REVERT: D 161 ASN cc_start: 0.6787 (m110) cc_final: 0.6309 (m110) REVERT: E 26 PHE cc_start: 0.7643 (m-80) cc_final: 0.7143 (m-80) REVERT: E 130 ASN cc_start: 0.7607 (t0) cc_final: 0.7294 (t0) REVERT: F 8 ILE cc_start: 0.7057 (mp) cc_final: 0.6821 (mp) REVERT: F 33 TYR cc_start: 0.8396 (m-80) cc_final: 0.7619 (m-10) REVERT: F 98 LEU cc_start: 0.7808 (mm) cc_final: 0.7372 (mm) REVERT: G 66 VAL cc_start: 0.8899 (t) cc_final: 0.8657 (t) REVERT: G 125 MET cc_start: 0.7674 (mtm) cc_final: 0.7199 (mtp) REVERT: G 126 ASP cc_start: 0.8887 (m-30) cc_final: 0.8565 (m-30) REVERT: H 1 MET cc_start: 0.2537 (ptm) cc_final: 0.2099 (ptm) REVERT: H 20 TYR cc_start: 0.7877 (m-10) cc_final: 0.7669 (m-10) REVERT: H 61 VAL cc_start: 0.8278 (t) cc_final: 0.8008 (t) REVERT: I 33 PHE cc_start: 0.5750 (t80) cc_final: 0.5351 (t80) REVERT: J 14 LYS cc_start: 0.9269 (pptt) cc_final: 0.8801 (pptt) REVERT: J 72 VAL cc_start: 0.7180 (p) cc_final: 0.6963 (p) REVERT: K 66 LEU cc_start: 0.8365 (mt) cc_final: 0.7863 (mt) REVERT: K 124 LYS cc_start: 0.8077 (ttmt) cc_final: 0.7804 (ttmt) REVERT: L 60 LEU cc_start: 0.8969 (tp) cc_final: 0.8607 (tp) REVERT: L 84 LEU cc_start: 0.6218 (tp) cc_final: 0.5708 (tp) REVERT: O 7 GLU cc_start: 0.8147 (pt0) cc_final: 0.7573 (pt0) REVERT: O 10 LYS cc_start: 0.9628 (pptt) cc_final: 0.9127 (pptt) REVERT: O 36 ILE cc_start: 0.8287 (mm) cc_final: 0.8040 (mm) REVERT: O 58 MET cc_start: 0.8052 (tmm) cc_final: 0.7808 (tpt) REVERT: O 59 MET cc_start: 0.8664 (mmt) cc_final: 0.8454 (mmp) REVERT: P 49 LEU cc_start: 0.8646 (tt) cc_final: 0.8392 (tt) REVERT: Q 5 VAL cc_start: 0.7967 (t) cc_final: 0.7752 (t) REVERT: Q 60 ILE cc_start: 0.7267 (tp) cc_final: 0.7058 (tp) REVERT: R 30 ASP cc_start: 0.7248 (t0) cc_final: 0.6526 (t0) REVERT: R 66 LEU cc_start: 0.9169 (tp) cc_final: 0.8839 (tp) REVERT: R 68 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7619 (mmmt) REVERT: S 18 LYS cc_start: 0.8129 (mttt) cc_final: 0.7624 (mtpt) REVERT: T 36 LEU cc_start: 0.8624 (mm) cc_final: 0.8290 (tp) REVERT: T 72 LEU cc_start: 0.7781 (tp) cc_final: 0.7523 (tp) REVERT: T 73 HIS cc_start: 0.5800 (m90) cc_final: 0.5200 (m-70) REVERT: T 86 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7582 (ttt180) REVERT: X 22 ASP cc_start: 0.6887 (p0) cc_final: 0.6662 (p0) REVERT: a 79 MET cc_start: 0.3961 (ptt) cc_final: 0.3687 (ttt) REVERT: a 228 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7892 (mt-10) REVERT: a 465 MET cc_start: -0.0108 (ptt) cc_final: -0.0904 (ptt) outliers start: 1 outliers final: 0 residues processed: 621 average time/residue: 0.6673 time to fit residues: 665.3756 Evaluate side-chains 481 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 430 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 325 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 375 optimal weight: 5.9990 chunk 249 optimal weight: 30.0000 chunk 444 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN C 118 GLN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 8 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS O 62 GLN ** P 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 16 HIS T 45 GLN a 109 HIS a 119 GLN ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 63974 Z= 0.213 Angle : 0.724 13.392 94338 Z= 0.381 Chirality : 0.038 0.292 11767 Planarity : 0.006 0.118 6019 Dihedral : 25.312 179.683 29119 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 33.82 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.33 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.56 (0.14), residues: 3071 helix: 0.14 (0.15), residues: 1118 sheet: -0.99 (0.21), residues: 568 loop : -2.03 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 59 HIS 0.018 0.002 HIS K 116 PHE 0.042 0.003 PHE B 55 TYR 0.027 0.002 TYR P 17 ARG 0.009 0.001 ARG O 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 617 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8585 (tp) cc_final: 0.8300 (tp) REVERT: C 67 THR cc_start: 0.6384 (m) cc_final: 0.5411 (m) REVERT: D 84 LYS cc_start: 0.7850 (tttt) cc_final: 0.7607 (tttt) REVERT: D 161 ASN cc_start: 0.6374 (m110) cc_final: 0.5844 (m110) REVERT: E 26 PHE cc_start: 0.7436 (m-80) cc_final: 0.6930 (m-80) REVERT: E 130 ASN cc_start: 0.7462 (t0) cc_final: 0.7164 (t0) REVERT: F 33 TYR cc_start: 0.8356 (m-80) cc_final: 0.7761 (m-10) REVERT: G 31 MET cc_start: 0.7900 (ttt) cc_final: 0.7017 (ttt) REVERT: G 38 LEU cc_start: 0.8821 (tp) cc_final: 0.8425 (tp) REVERT: H 1 MET cc_start: 0.2856 (ptm) cc_final: 0.2358 (ptm) REVERT: H 20 TYR cc_start: 0.7908 (m-10) cc_final: 0.7440 (m-10) REVERT: H 61 VAL cc_start: 0.8332 (t) cc_final: 0.8106 (t) REVERT: I 33 PHE cc_start: 0.5787 (t80) cc_final: 0.5311 (t80) REVERT: J 14 LYS cc_start: 0.9290 (pptt) cc_final: 0.8828 (pptt) REVERT: K 66 LEU cc_start: 0.8402 (mt) cc_final: 0.7849 (mt) REVERT: K 81 ASP cc_start: 0.8072 (t0) cc_final: 0.7303 (t0) REVERT: K 124 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7586 (ttmt) REVERT: L 60 LEU cc_start: 0.9073 (tp) cc_final: 0.8622 (tp) REVERT: N 34 TYR cc_start: 0.7095 (t80) cc_final: 0.6791 (t80) REVERT: N 47 LEU cc_start: 0.8536 (tp) cc_final: 0.8269 (tp) REVERT: N 58 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7912 (ptmt) REVERT: O 7 GLU cc_start: 0.8403 (pt0) cc_final: 0.7861 (pt0) REVERT: O 10 LYS cc_start: 0.9592 (pptt) cc_final: 0.9243 (pptt) REVERT: O 32 LEU cc_start: 0.7390 (mt) cc_final: 0.7131 (mt) REVERT: O 59 MET cc_start: 0.8608 (mmt) cc_final: 0.8103 (mtp) REVERT: O 66 LEU cc_start: 0.8019 (mm) cc_final: 0.7814 (mm) REVERT: O 70 LEU cc_start: 0.9006 (tp) cc_final: 0.8582 (tp) REVERT: O 81 LEU cc_start: 0.8705 (mm) cc_final: 0.8229 (mm) REVERT: Q 5 VAL cc_start: 0.8055 (t) cc_final: 0.7797 (t) REVERT: R 30 ASP cc_start: 0.6856 (t0) cc_final: 0.5866 (t70) REVERT: R 66 LEU cc_start: 0.9182 (tp) cc_final: 0.8794 (tp) REVERT: R 75 ILE cc_start: 0.8318 (mm) cc_final: 0.7923 (mm) REVERT: S 15 LEU cc_start: 0.8485 (pp) cc_final: 0.8088 (pp) REVERT: S 18 LYS cc_start: 0.8152 (mttt) cc_final: 0.7626 (mtpt) REVERT: T 36 LEU cc_start: 0.8833 (mm) cc_final: 0.8325 (tp) REVERT: T 73 HIS cc_start: 0.5860 (m90) cc_final: 0.5288 (m-70) REVERT: W 42 MET cc_start: 0.6136 (mtm) cc_final: 0.5463 (mmm) REVERT: X 163 MET cc_start: 0.6626 (tpt) cc_final: 0.6207 (tpp) REVERT: a 79 MET cc_start: 0.5058 (ptt) cc_final: 0.4158 (ttt) REVERT: a 228 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7860 (mp0) REVERT: a 465 MET cc_start: -0.0203 (ptt) cc_final: -0.1156 (ptt) outliers start: 0 outliers final: 0 residues processed: 617 average time/residue: 0.6577 time to fit residues: 652.6184 Evaluate side-chains 466 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 274 optimal weight: 6.9990 chunk 177 optimal weight: 0.9980 chunk 265 optimal weight: 30.0000 chunk 133 optimal weight: 30.0000 chunk 87 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 282 optimal weight: 40.0000 chunk 302 optimal weight: 30.0000 chunk 219 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 349 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 8 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS ** T 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 63974 Z= 0.231 Angle : 0.740 13.414 94338 Z= 0.388 Chirality : 0.039 0.306 11767 Planarity : 0.007 0.118 6019 Dihedral : 25.375 179.985 29119 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 37.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.90 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3071 helix: 0.07 (0.15), residues: 1119 sheet: -0.96 (0.21), residues: 552 loop : -2.07 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 173 HIS 0.019 0.002 HIS K 116 PHE 0.031 0.003 PHE K 125 TYR 0.027 0.002 TYR P 58 ARG 0.012 0.001 ARG P 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 611 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8445 (tp) cc_final: 0.8163 (tp) REVERT: B 215 LEU cc_start: 0.9201 (tp) cc_final: 0.8989 (tp) REVERT: C 67 THR cc_start: 0.6351 (m) cc_final: 0.5264 (m) REVERT: D 84 LYS cc_start: 0.7841 (tttt) cc_final: 0.7603 (tttt) REVERT: D 161 ASN cc_start: 0.6907 (m110) cc_final: 0.6264 (m110) REVERT: E 26 PHE cc_start: 0.7806 (m-80) cc_final: 0.7088 (m-80) REVERT: E 130 ASN cc_start: 0.7548 (t0) cc_final: 0.7121 (t0) REVERT: F 33 TYR cc_start: 0.8147 (m-80) cc_final: 0.7889 (m-10) REVERT: G 31 MET cc_start: 0.7931 (ttt) cc_final: 0.7434 (ttt) REVERT: G 66 VAL cc_start: 0.8945 (t) cc_final: 0.8721 (t) REVERT: H 61 VAL cc_start: 0.8354 (t) cc_final: 0.8145 (t) REVERT: I 33 PHE cc_start: 0.5982 (t80) cc_final: 0.5539 (t80) REVERT: J 14 LYS cc_start: 0.9345 (pptt) cc_final: 0.8883 (pptt) REVERT: K 66 LEU cc_start: 0.8423 (mt) cc_final: 0.7834 (mt) REVERT: K 67 ASP cc_start: 0.8238 (t0) cc_final: 0.7753 (t0) REVERT: K 81 ASP cc_start: 0.7659 (t0) cc_final: 0.7210 (t0) REVERT: L 60 LEU cc_start: 0.8893 (tp) cc_final: 0.8498 (tp) REVERT: N 34 TYR cc_start: 0.6930 (t80) cc_final: 0.6711 (t80) REVERT: O 7 GLU cc_start: 0.8311 (pt0) cc_final: 0.7641 (pt0) REVERT: O 10 LYS cc_start: 0.9532 (pptt) cc_final: 0.9206 (pptt) REVERT: O 58 MET cc_start: 0.7886 (tmm) cc_final: 0.6699 (tmm) REVERT: O 66 LEU cc_start: 0.8064 (mm) cc_final: 0.7834 (mm) REVERT: O 70 LEU cc_start: 0.8992 (tp) cc_final: 0.8232 (tp) REVERT: P 55 ARG cc_start: 0.7900 (tpm170) cc_final: 0.7333 (tpm170) REVERT: Q 5 VAL cc_start: 0.8085 (t) cc_final: 0.7799 (t) REVERT: R 30 ASP cc_start: 0.6733 (t0) cc_final: 0.6116 (t70) REVERT: R 66 LEU cc_start: 0.9083 (tp) cc_final: 0.8770 (tp) REVERT: S 15 LEU cc_start: 0.8649 (pp) cc_final: 0.8099 (pp) REVERT: S 18 LYS cc_start: 0.8339 (mttt) cc_final: 0.7787 (mtpt) REVERT: T 36 LEU cc_start: 0.8843 (mm) cc_final: 0.8375 (tp) REVERT: T 73 HIS cc_start: 0.5901 (m90) cc_final: 0.5394 (m90) REVERT: a 79 MET cc_start: 0.5037 (ptt) cc_final: 0.4583 (ttt) REVERT: a 335 ILE cc_start: 0.7742 (mm) cc_final: 0.7415 (mm) REVERT: a 465 MET cc_start: -0.0225 (ptt) cc_final: -0.0933 (ptt) outliers start: 0 outliers final: 0 residues processed: 611 average time/residue: 0.6631 time to fit residues: 658.8199 Evaluate side-chains 461 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 461 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 404 optimal weight: 50.0000 chunk 425 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 chunk 414 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 374 optimal weight: 30.0000 chunk 391 optimal weight: 9.9990 chunk 412 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 63974 Z= 0.290 Angle : 0.822 13.493 94338 Z= 0.430 Chirality : 0.042 0.315 11767 Planarity : 0.007 0.120 6019 Dihedral : 25.668 179.734 29119 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 45.56 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.53 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.97 (0.14), residues: 3071 helix: -0.37 (0.14), residues: 1131 sheet: -1.11 (0.21), residues: 531 loop : -2.16 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 97 HIS 0.023 0.002 HIS K 116 PHE 0.036 0.003 PHE B 70 TYR 0.031 0.003 TYR P 17 ARG 0.060 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 588 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 THR cc_start: 0.7154 (m) cc_final: 0.6410 (m) REVERT: C 173 VAL cc_start: 0.8808 (t) cc_final: 0.8601 (t) REVERT: D 93 PHE cc_start: 0.6641 (t80) cc_final: 0.5958 (t80) REVERT: D 161 ASN cc_start: 0.6481 (m110) cc_final: 0.6059 (m110) REVERT: E 26 PHE cc_start: 0.7766 (m-80) cc_final: 0.6986 (m-80) REVERT: E 32 VAL cc_start: 0.7896 (p) cc_final: 0.7677 (p) REVERT: E 130 ASN cc_start: 0.7704 (t0) cc_final: 0.7386 (t0) REVERT: F 8 ILE cc_start: 0.7168 (mp) cc_final: 0.6941 (mp) REVERT: F 33 TYR cc_start: 0.8220 (m-80) cc_final: 0.7953 (m-10) REVERT: F 75 LEU cc_start: 0.9408 (pp) cc_final: 0.9194 (pp) REVERT: G 31 MET cc_start: 0.8635 (ttt) cc_final: 0.8230 (ttt) REVERT: G 43 PHE cc_start: 0.7411 (t80) cc_final: 0.6805 (t80) REVERT: H 20 TYR cc_start: 0.7894 (m-80) cc_final: 0.7654 (m-10) REVERT: H 61 VAL cc_start: 0.8319 (t) cc_final: 0.8103 (t) REVERT: H 107 LEU cc_start: 0.4789 (mm) cc_final: 0.4419 (mt) REVERT: I 33 PHE cc_start: 0.6359 (t80) cc_final: 0.5917 (t80) REVERT: I 109 VAL cc_start: 0.8533 (t) cc_final: 0.8327 (p) REVERT: J 14 LYS cc_start: 0.9394 (pptt) cc_final: 0.8876 (pptt) REVERT: K 66 LEU cc_start: 0.8483 (mt) cc_final: 0.7965 (mt) REVERT: K 124 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8110 (ttmt) REVERT: L 60 LEU cc_start: 0.8614 (tp) cc_final: 0.8261 (tp) REVERT: M 25 ILE cc_start: 0.6435 (mt) cc_final: 0.6200 (mt) REVERT: M 82 MET cc_start: 0.7389 (tmm) cc_final: 0.6122 (mmt) REVERT: N 34 TYR cc_start: 0.7007 (t80) cc_final: 0.6778 (t80) REVERT: N 58 LYS cc_start: 0.8554 (ptmt) cc_final: 0.8033 (ptmt) REVERT: O 7 GLU cc_start: 0.8358 (pt0) cc_final: 0.7678 (pt0) REVERT: O 10 LYS cc_start: 0.9532 (pptt) cc_final: 0.9148 (pptt) REVERT: O 32 LEU cc_start: 0.7646 (mt) cc_final: 0.7300 (mt) REVERT: O 36 ILE cc_start: 0.8244 (mm) cc_final: 0.7963 (mm) REVERT: O 59 MET cc_start: 0.8035 (mmp) cc_final: 0.7648 (mmm) REVERT: O 66 LEU cc_start: 0.8155 (mm) cc_final: 0.7914 (mm) REVERT: O 70 LEU cc_start: 0.9070 (tp) cc_final: 0.8670 (tp) REVERT: R 30 ASP cc_start: 0.6915 (t0) cc_final: 0.6342 (t70) REVERT: R 66 LEU cc_start: 0.9160 (tp) cc_final: 0.8597 (tp) REVERT: S 15 LEU cc_start: 0.8684 (pp) cc_final: 0.7779 (pp) REVERT: S 17 GLU cc_start: 0.8102 (pt0) cc_final: 0.7630 (pp20) REVERT: T 36 LEU cc_start: 0.8828 (mm) cc_final: 0.8335 (tp) REVERT: T 73 HIS cc_start: 0.5895 (m90) cc_final: 0.5390 (m90) REVERT: X 41 MET cc_start: -0.3514 (mtm) cc_final: -0.3816 (mtm) outliers start: 0 outliers final: 0 residues processed: 588 average time/residue: 0.6340 time to fit residues: 607.1754 Evaluate side-chains 442 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 271 optimal weight: 7.9990 chunk 437 optimal weight: 20.0000 chunk 267 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 459 optimal weight: 50.0000 chunk 422 optimal weight: 30.0000 chunk 365 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 282 optimal weight: 0.4980 chunk 224 optimal weight: 5.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 16 HIS ** a 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 GLN a 265 ASN ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.8066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63974 Z= 0.208 Angle : 0.747 14.645 94338 Z= 0.392 Chirality : 0.039 0.314 11767 Planarity : 0.007 0.127 6019 Dihedral : 25.564 179.745 29119 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 35.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.90 % Favored : 92.67 % Rotamer: Outliers : 0.04 % Allowed : 0.43 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.79 (0.14), residues: 3071 helix: -0.21 (0.15), residues: 1134 sheet: -1.00 (0.21), residues: 547 loop : -2.09 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 64 HIS 0.017 0.002 HIS K 116 PHE 0.021 0.002 PHE B 55 TYR 0.038 0.002 TYR P 58 ARG 0.018 0.001 ARG J 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6142 Ramachandran restraints generated. 3071 Oldfield, 0 Emsley, 3071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 587 time to evaluate : 3.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 LEU cc_start: 0.8677 (tp) cc_final: 0.8422 (tp) REVERT: D 158 ILE cc_start: 0.6701 (pt) cc_final: 0.6413 (pt) REVERT: E 26 PHE cc_start: 0.7877 (m-80) cc_final: 0.7368 (m-80) REVERT: F 75 LEU cc_start: 0.9480 (pp) cc_final: 0.9181 (pp) REVERT: G 31 MET cc_start: 0.8554 (ttt) cc_final: 0.8345 (ttt) REVERT: G 43 PHE cc_start: 0.7288 (t80) cc_final: 0.6698 (t80) REVERT: H 107 LEU cc_start: 0.5254 (mm) cc_final: 0.4868 (mt) REVERT: I 33 PHE cc_start: 0.5931 (t80) cc_final: 0.5494 (t80) REVERT: I 109 VAL cc_start: 0.8426 (t) cc_final: 0.8222 (p) REVERT: J 14 LYS cc_start: 0.9322 (pptt) cc_final: 0.8608 (pptt) REVERT: K 66 LEU cc_start: 0.8421 (mt) cc_final: 0.7885 (mt) REVERT: K 81 ASP cc_start: 0.7305 (t0) cc_final: 0.7044 (t0) REVERT: L 60 LEU cc_start: 0.8593 (tp) cc_final: 0.8324 (tp) REVERT: L 93 LEU cc_start: 0.8333 (mt) cc_final: 0.8035 (mt) REVERT: N 34 TYR cc_start: 0.7083 (t80) cc_final: 0.6837 (t80) REVERT: O 7 GLU cc_start: 0.8347 (pt0) cc_final: 0.7339 (pt0) REVERT: O 10 LYS cc_start: 0.9451 (pptt) cc_final: 0.9020 (pptt) REVERT: O 66 LEU cc_start: 0.8010 (mm) cc_final: 0.7756 (mm) REVERT: O 70 LEU cc_start: 0.8999 (tp) cc_final: 0.8266 (tp) REVERT: Q 86 GLU cc_start: 0.9454 (mp0) cc_final: 0.9205 (mp0) REVERT: R 30 ASP cc_start: 0.6681 (t0) cc_final: 0.6132 (t70) REVERT: S 15 LEU cc_start: 0.8680 (pp) cc_final: 0.7778 (pp) REVERT: S 17 GLU cc_start: 0.7964 (pt0) cc_final: 0.7486 (pp20) REVERT: T 36 LEU cc_start: 0.8768 (mm) cc_final: 0.8291 (tp) REVERT: T 73 HIS cc_start: 0.5745 (m90) cc_final: 0.5179 (m90) REVERT: W 70 ARG cc_start: 0.7149 (mpp-170) cc_final: 0.6805 (mmt180) REVERT: X 41 MET cc_start: -0.2992 (mtm) cc_final: -0.3309 (mtm) REVERT: a 79 MET cc_start: 0.0130 (ttt) cc_final: -0.0666 (tpp) outliers start: 1 outliers final: 0 residues processed: 588 average time/residue: 0.6604 time to fit residues: 636.5625 Evaluate side-chains 446 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 461 random chunks: chunk 290 optimal weight: 10.0000 chunk 389 optimal weight: 0.0010 chunk 112 optimal weight: 30.0000 chunk 337 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 366 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 46 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 overall best weight: 5.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 108 ASN ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 16 HIS ** a 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 119 GLN ** a 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.063656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.050941 restraints weight = 392935.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054093 restraints weight = 164677.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.056148 restraints weight = 85950.887| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.8264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 63974 Z= 0.219 Angle : 0.744 13.966 94338 Z= 0.390 Chirality : 0.039 0.319 11767 Planarity : 0.007 0.118 6019 Dihedral : 25.518 179.666 29119 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 37.21 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.04 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % 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: -1.78 (0.14), residues: 3071 helix: -0.20 (0.15), residues: 1136 sheet: -0.97 (0.21), residues: 556 loop : -2.10 (0.16), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 173 HIS 0.018 0.002 HIS K 116 PHE 0.027 0.003 PHE B 17 TYR 0.024 0.002 TYR C 23 ARG 0.031 0.001 ARG R 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11941.38 seconds wall clock time: 213 minutes 26.79 seconds (12806.79 seconds total)