Starting phenix.real_space_refine on Fri Dec 8 05:36:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmr_4077/12_2023/5lmr_4077_neut_updated.pdb" } resolution = 4.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 1605 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 28676 2.51 5 N 10484 2.21 5 O 14832 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 12": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "O GLU 6": "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 83": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "W ARG 46": "NH1" <-> "NH2" Residue "X GLU 84": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 55662 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 32542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32542 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "', 'pdbres=" A A 914 "', 'pdbres=" C A1397 "'] Classifications: {'RNA': 1515} Modifications used: {'5*END': 4, 'rna2p_pur': 106, 'rna2p_pyr': 77, 'rna3p_pur': 749, 'rna3p_pyr': 583} Link IDs: {'rna2p': 183, 'rna3p': 1331} Chain breaks: 7 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: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} 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: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1356 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 373 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain breaks: 1 Chain: "Z" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 12, 'rna3p': 64} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36113 SG CYS D 9 85.731 102.895 147.855 1.00 50.00 S ATOM 36256 SG CYS D 26 82.670 104.504 148.028 1.00 50.00 S ATOM 36296 SG CYS D 31 84.935 106.175 147.376 1.00 50.00 S ATOM 46931 SG CYS N 24 153.218 113.577 132.984 1.00 50.00 S ATOM 46955 SG CYS N 27 151.743 110.435 131.700 1.00 50.00 S ATOM 47062 SG CYS N 40 152.289 113.480 129.272 1.00 50.00 S ATOM 47087 SG CYS N 43 149.373 113.591 131.523 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: 24.44, per 1000 atoms: 0.44 Number of scatterers: 55662 At special positions: 0 Unit cell: (227.8, 180.9, 203.68, 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 61 16.00 P 1605 15.00 Mg 2 11.99 O 14832 8.00 N 10484 7.00 C 28676 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=0, symmetry=0 Time building additional restraints: 27.99 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " Number of angles added : 6 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 26 sheets defined 34.2% alpha, 15.9% beta 524 base pairs and 911 stacking pairs defined. Time for finding SS restraints: 27.67 Creating SS restraints... Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.609A pdb=" N ALA B 29 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG B 30 " --> pdb=" O LYS B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 44 through 64 removed outlier: 3.727A pdb=" N ARG B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.016A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.688A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 10 No H-bonds generated for 'chain 'C' and resid 7 through 10' 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 removed outlier: 3.568A pdb=" N ARG C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 125 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 Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 114 through 123 Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.791A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 4.499A 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 69 through 81 removed outlier: 5.106A pdb=" N ASN F 73 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 3.569A pdb=" N ARG G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 3.601A pdb=" N PHE G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 133 through 151 removed outlier: 4.274A pdb=" N GLU G 146 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA G 147 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 103 through 105 No H-bonds generated for 'chain 'H' and resid 103 through 105' Processing helix chain 'H' and resid 121 through 126 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 42 through 52 Proline residue: I 49 - end of helix Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 93 through 96 No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'J' and resid 17 through 28 removed outlier: 4.160A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 27 " --> pdb=" O ILE J 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 55 No H-bonds generated for 'chain 'K' and resid 53 through 55' Processing helix chain 'K' and resid 58 through 75 removed outlier: 3.776A pdb=" N TYR K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 100 Processing helix chain 'L' and resid 7 through 13 Processing helix chain 'L' and resid 117 through 119 No H-bonds generated for 'chain 'L' and resid 117 through 119' Processing helix chain 'M' and resid 15 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 61 Processing helix chain 'M' and resid 67 through 82 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 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 41 through 50 Processing helix chain 'O' and resid 5 through 15 removed outlier: 3.504A pdb=" N VAL O 11 " --> pdb=" O GLU O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.598A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 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 82 through 97 removed outlier: 3.680A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) 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 13 through 19 removed outlier: 3.820A pdb=" N GLU S 17 " --> pdb=" O ASP S 13 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS S 18 " --> pdb=" O HIS S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 74 No H-bonds generated for 'chain 'S' and resid 72 through 74' Processing helix chain 'T' and resid 11 through 46 removed outlier: 3.583A pdb=" N LYS T 14 " --> pdb=" O SER T 11 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA T 32 " --> pdb=" O LYS T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 69 Processing helix chain 'T' and resid 76 through 92 Processing helix chain 'V' and resid 9 through 15 Processing helix chain 'W' and resid 38 through 42 Processing helix chain 'X' and resid 31 through 41 Processing helix chain 'X' and resid 62 through 79 Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 129 through 143 Processing sheet with id= A, first strand: chain 'B' and resid 68 through 71 removed outlier: 7.023A pdb=" N ALA B 161 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL B 71 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 163 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL B 164 " --> pdb=" O PRO B 183 " (cutoff:3.500A) removed outlier: 6.803A 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 'B' and resid 32 through 36 removed outlier: 6.629A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.628A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= F, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= G, first strand: chain 'E' and resid 7 through 10 Processing sheet with id= H, first strand: chain 'E' and resid 80 through 84 Processing sheet with id= I, first strand: chain 'F' and resid 44 through 47 Processing sheet with id= J, first strand: chain 'F' and resid 36 through 41 removed outlier: 6.795A pdb=" N GLN F 64 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL F 40 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TRP F 62 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 73 through 79 Processing sheet with id= L, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.558A pdb=" N THR H 24 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU H 49 " --> pdb=" O ARG H 60 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY H 47 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 82 through 85 removed outlier: 6.871A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 3 through 10 Processing sheet with id= O, first strand: chain 'J' and resid 68 through 74 removed outlier: 3.534A pdb=" N VAL J 72 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 46 through 50 Processing sheet with id= Q, first strand: chain 'K' and resid 39 through 44 removed outlier: 6.853A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER K 44 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR K 28 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG K 85 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLN K 104 " --> pdb=" O VAL K 80 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL K 82 " --> pdb=" O GLN K 104 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS K 106 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 12.003A pdb=" N VAL K 84 " --> pdb=" O LYS K 106 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N ILE K 108 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 82 through 85 removed outlier: 3.988A pdb=" N ARG L 97 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR L 69 " --> pdb=" O ARG L 97 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N HIS L 99 " --> pdb=" O TYR L 69 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 40 through 43 Processing sheet with id= T, first strand: chain 'P' and resid 2 through 5 removed outlier: 6.710A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS P 50 " --> pdb=" O TYR P 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Q' and resid 71 through 73 removed outlier: 14.737A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE Q 27 " --> pdb=" O ILE Q 36 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'Q' and resid 56 through 58 removed outlier: 6.043A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= X, first strand: chain 'W' and resid 52 through 57 removed outlier: 6.464A pdb=" N ARG W 23 " --> pdb=" O THR W 14 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ALA W 16 " --> pdb=" O THR W 21 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR W 21 " --> pdb=" O ALA W 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL W 24 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'X' and resid 25 through 30 removed outlier: 6.388A pdb=" N VAL X 18 " --> pdb=" O LEU X 26 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE X 28 " --> pdb=" O VAL X 16 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL X 16 " --> pdb=" O ILE X 28 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET X 60 " --> pdb=" O LEU X 45 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU X 45 " --> pdb=" O MET X 60 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'X' and resid 85 through 90 removed outlier: 5.937A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU X 164 " --> pdb=" O MET X 152 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) 787 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1403 hydrogen bonds 2408 hydrogen bond angles 0 basepair planarities 524 basepair parallelities 911 stacking parallelities Total time for adding SS restraints: 37.69 Time building geometry restraints manager: 29.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9135 1.33 - 1.45: 23832 1.45 - 1.58: 23835 1.58 - 1.70: 3193 1.70 - 1.82: 107 Bond restraints: 60102 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.494 0.308 2.00e-02 2.50e+03 2.36e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.359 0.276 2.00e-02 2.50e+03 1.90e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.412 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.342 0.156 2.00e-02 2.50e+03 6.07e+01 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.337 -0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 60097 not shown) Histogram of bond angle deviations from ideal: 79.19 - 90.97: 6 90.97 - 102.76: 3311 102.76 - 114.55: 42877 114.55 - 126.34: 37916 126.34 - 138.13: 4962 Bond angle restraints: 89072 Sorted by residual: angle pdb=" N ARG W 23 " pdb=" CA ARG W 23 " pdb=" C ARG W 23 " ideal model delta sigma weight residual 110.20 79.19 31.01 1.58e+00 4.01e-01 3.85e+02 angle pdb=" C ARG E 15 " pdb=" CA ARG E 15 " pdb=" CB ARG E 15 " ideal model delta sigma weight residual 109.72 85.65 24.07 1.73e+00 3.34e-01 1.94e+02 angle pdb=" N ARG E 15 " pdb=" CA ARG E 15 " pdb=" C ARG E 15 " ideal model delta sigma weight residual 109.07 87.37 21.70 1.61e+00 3.86e-01 1.82e+02 angle pdb=" C ALA C 65 " pdb=" CA ALA C 65 " pdb=" CB ALA C 65 " ideal model delta sigma weight residual 109.72 87.83 21.89 1.73e+00 3.34e-01 1.60e+02 angle pdb=" O3' C A1145 " pdb=" C3' C A1145 " pdb=" C2' C A1145 " ideal model delta sigma weight residual 109.50 126.74 -17.24 1.50e+00 4.44e-01 1.32e+02 ... (remaining 89067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 32627 35.87 - 71.74: 4574 71.74 - 107.61: 616 107.61 - 143.48: 29 143.48 - 179.35: 42 Dihedral angle restraints: 37888 sinusoidal: 30342 harmonic: 7546 Sorted by residual: dihedral pdb=" C ARG E 15 " pdb=" N ARG E 15 " pdb=" CA ARG E 15 " pdb=" CB ARG E 15 " ideal model delta harmonic sigma weight residual -122.60 -84.48 -38.12 0 2.50e+00 1.60e-01 2.33e+02 dihedral pdb=" C ALA C 65 " pdb=" N ALA C 65 " pdb=" CA ALA C 65 " pdb=" CB ALA C 65 " ideal model delta harmonic sigma weight residual -122.60 -87.97 -34.63 0 2.50e+00 1.60e-01 1.92e+02 dihedral pdb=" C5' A A 559 " pdb=" C4' A A 559 " pdb=" C3' A A 559 " pdb=" O3' A A 559 " ideal model delta sinusoidal sigma weight residual 147.00 63.29 83.71 1 8.00e+00 1.56e-02 1.34e+02 ... (remaining 37885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 10312 0.213 - 0.425: 802 0.425 - 0.638: 27 0.638 - 0.851: 17 0.851 - 1.063: 5 Chirality restraints: 11163 Sorted by residual: chirality pdb=" C3' G A 115 " pdb=" C4' G A 115 " pdb=" O3' G A 115 " pdb=" C2' G A 115 " both_signs ideal model delta sigma weight residual False -2.74 -1.68 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" C3' U A1065 " pdb=" C4' U A1065 " pdb=" O3' U A1065 " pdb=" C2' U A1065 " both_signs ideal model delta sigma weight residual False -2.74 -1.81 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C3' U A1498 " pdb=" C4' U A1498 " pdb=" O3' U A1498 " pdb=" C2' U A1498 " both_signs ideal model delta sigma weight residual False -2.74 -1.82 -0.93 2.00e-01 2.50e+01 2.14e+01 ... (remaining 11160 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 4SU Z 8 " -0.010 2.00e-02 2.50e+03 5.81e-01 7.60e+03 pdb=" C4' 4SU Z 8 " 0.480 2.00e-02 2.50e+03 pdb=" O4' 4SU Z 8 " 0.715 2.00e-02 2.50e+03 pdb=" C3' 4SU Z 8 " -0.541 2.00e-02 2.50e+03 pdb=" O3' 4SU Z 8 " -0.565 2.00e-02 2.50e+03 pdb=" C2' 4SU Z 8 " -0.205 2.00e-02 2.50e+03 pdb=" O2' 4SU Z 8 " 0.842 2.00e-02 2.50e+03 pdb=" C1' 4SU Z 8 " 0.224 2.00e-02 2.50e+03 pdb=" N1 4SU Z 8 " -0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' G7M Z 46 " 0.806 2.00e-02 2.50e+03 5.37e-01 6.49e+03 pdb=" C4' G7M Z 46 " -0.250 2.00e-02 2.50e+03 pdb=" O4' G7M Z 46 " -0.564 2.00e-02 2.50e+03 pdb=" C3' G7M Z 46 " 0.213 2.00e-02 2.50e+03 pdb=" O3' G7M Z 46 " -0.883 2.00e-02 2.50e+03 pdb=" C2' G7M Z 46 " 0.582 2.00e-02 2.50e+03 pdb=" O2' G7M Z 46 " 0.507 2.00e-02 2.50e+03 pdb=" C1' G7M Z 46 " -0.381 2.00e-02 2.50e+03 pdb=" N9 G7M Z 46 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU Z 54 " 0.119 2.00e-02 2.50e+03 5.33e-01 6.39e+03 pdb=" C4' 5MU Z 54 " -0.471 2.00e-02 2.50e+03 pdb=" O4' 5MU Z 54 " -0.761 2.00e-02 2.50e+03 pdb=" C3' 5MU Z 54 " 0.498 2.00e-02 2.50e+03 pdb=" O3' 5MU Z 54 " 0.422 2.00e-02 2.50e+03 pdb=" C2' 5MU Z 54 " 0.279 2.00e-02 2.50e+03 pdb=" O2' 5MU Z 54 " -0.701 2.00e-02 2.50e+03 pdb=" C1' 5MU Z 54 " -0.219 2.00e-02 2.50e+03 pdb=" N1 5MU Z 54 " 0.836 2.00e-02 2.50e+03 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 13 2.12 - 2.82: 12459 2.82 - 3.51: 82099 3.51 - 4.21: 183351 4.21 - 4.90: 238283 Nonbonded interactions: 516205 Sorted by model distance: nonbonded pdb=" OP2 U A1257 " pdb=" NZ LYS C 27 " model vdw 1.426 2.520 nonbonded pdb=" O4 U A1358 " pdb=" N1 A A1363A" model vdw 1.751 2.496 nonbonded pdb=" N3 U A1345 " pdb=" N6 A A1375 " model vdw 1.871 2.560 nonbonded pdb=" O ALA C 92 " pdb=" O THR C 95 " model vdw 1.871 3.040 nonbonded pdb=" O4 U A 827 " pdb=" N1 A A 872 " model vdw 1.906 2.496 ... (remaining 516200 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.800 Check model and map are aligned: 0.600 Set scattering table: 0.380 Process input model: 167.990 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 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 0.308 60102 Z= 0.500 Angle : 1.387 31.014 89072 Z= 0.928 Chirality : 0.117 1.063 11163 Planarity : 0.017 0.581 5332 Dihedral : 25.987 179.352 33038 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 2.79 % Allowed : 8.67 % Favored : 88.54 % Rotamer: Outliers : 16.73 % Allowed : 18.19 % Favored : 65.08 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.04 % 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: -2.16 (0.14), residues: 2584 helix: 0.19 (0.14), residues: 990 sheet: -1.70 (0.23), residues: 409 loop : -2.82 (0.15), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 24 HIS 0.010 0.002 HIS S 83 PHE 0.024 0.003 PHE G 62 TYR 0.028 0.003 TYR O 78 ARG 0.025 0.002 ARG P 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 992 time to evaluate : 2.627 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 outliers start: 368 outliers final: 71 residues processed: 1195 average time/residue: 0.6635 time to fit residues: 1245.0093 Evaluate side-chains 691 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 620 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.6097 time to fit residues: 74.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 347 optimal weight: 8.9990 chunk 311 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 166 optimal weight: 30.0000 chunk 322 optimal weight: 50.0000 chunk 124 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 373 optimal weight: 4.9990 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 19 HIS B 104 ASN B 113 HIS B 212 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 63 ASN C 102 ASN C 108 ASN C 176 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN D 125 HIS D 161 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN G 37 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS J 76 ASN J 78 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS N 49 HIS ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN S 53 ASN S 83 HIS ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 HIS X 100 GLN ** X 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 60102 Z= 0.318 Angle : 0.894 14.509 89072 Z= 0.473 Chirality : 0.048 0.390 11163 Planarity : 0.008 0.125 5332 Dihedral : 25.112 179.947 27547 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.74 % Favored : 91.37 % Rotamer: Outliers : 0.36 % Allowed : 6.78 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.73 (0.15), residues: 2584 helix: 0.52 (0.16), residues: 988 sheet: -1.41 (0.22), residues: 454 loop : -2.60 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 24 HIS 0.025 0.002 HIS K 116 PHE 0.033 0.003 PHE X 109 TYR 0.035 0.003 TYR M 21 ARG 0.016 0.001 ARG I 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 809 time to evaluate : 2.732 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 outliers start: 8 outliers final: 2 residues processed: 811 average time/residue: 0.6271 time to fit residues: 810.0645 Evaluate side-chains 574 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 572 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3825 time to fit residues: 4.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 207 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 373 optimal weight: 3.9990 chunk 403 optimal weight: 40.0000 chunk 332 optimal weight: 6.9990 chunk 370 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 299 optimal weight: 0.0370 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS B 146 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS D 62 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN G 96 GLN ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 9 GLN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS R 63 GLN ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 70 GLN X 97 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 60102 Z= 0.230 Angle : 0.769 14.197 89072 Z= 0.406 Chirality : 0.041 0.280 11163 Planarity : 0.007 0.115 5332 Dihedral : 24.881 178.464 27547 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.78 % Favored : 91.49 % Rotamer: Outliers : 0.32 % Allowed : 5.59 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.53 (0.16), residues: 2584 helix: 0.48 (0.16), residues: 977 sheet: -1.23 (0.23), residues: 458 loop : -2.28 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 24 HIS 0.014 0.002 HIS K 116 PHE 0.031 0.003 PHE W 22 TYR 0.032 0.002 TYR Q 95 ARG 0.015 0.001 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 765 time to evaluate : 2.680 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 outliers start: 7 outliers final: 2 residues processed: 769 average time/residue: 0.6135 time to fit residues: 759.9845 Evaluate side-chains 558 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 556 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4248 time to fit residues: 4.5633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 369 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 178 optimal weight: 0.3980 chunk 251 optimal weight: 0.4980 chunk 375 optimal weight: 9.9990 chunk 397 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN G 68 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 99 HIS ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN X 97 HIS ** X 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 60102 Z= 0.235 Angle : 0.746 14.486 89072 Z= 0.391 Chirality : 0.040 0.295 11163 Planarity : 0.007 0.117 5332 Dihedral : 24.744 177.719 27547 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.20 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.16 % Favored : 92.14 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.42 (0.16), residues: 2584 helix: 0.46 (0.16), residues: 972 sheet: -0.99 (0.24), residues: 428 loop : -2.16 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 59 HIS 0.022 0.002 HIS S 57 PHE 0.025 0.002 PHE B 17 TYR 0.023 0.002 TYR M 21 ARG 0.014 0.001 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 700 time to evaluate : 2.648 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 outliers start: 2 outliers final: 0 residues processed: 701 average time/residue: 0.5983 time to fit residues: 687.4240 Evaluate side-chains 531 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 531 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 330 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 163 optimal weight: 0.0980 chunk 339 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN F 84 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 60102 Z= 0.212 Angle : 0.715 14.550 89072 Z= 0.376 Chirality : 0.038 0.292 11163 Planarity : 0.007 0.119 5332 Dihedral : 24.635 178.338 27547 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 25.77 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.16 % Favored : 92.14 % Rotamer: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.36 (0.16), residues: 2584 helix: 0.40 (0.16), residues: 965 sheet: -0.89 (0.24), residues: 441 loop : -2.03 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 24 HIS 0.010 0.001 HIS K 116 PHE 0.021 0.002 PHE R 81 TYR 0.019 0.002 TYR Q 88 ARG 0.010 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 681 time to evaluate : 3.320 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 outliers start: 1 outliers final: 0 residues processed: 682 average time/residue: 0.5958 time to fit residues: 667.3555 Evaluate side-chains 510 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 133 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 397 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS S 14 HIS ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN W 43 HIS X 97 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 60102 Z= 0.329 Angle : 0.795 14.789 89072 Z= 0.413 Chirality : 0.041 0.343 11163 Planarity : 0.007 0.122 5332 Dihedral : 24.694 178.253 27547 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 35.86 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.63 % Favored : 90.67 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.74 (0.16), residues: 2584 helix: -0.04 (0.16), residues: 970 sheet: -1.11 (0.24), residues: 436 loop : -2.12 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 24 HIS 0.010 0.002 HIS K 116 PHE 0.020 0.002 PHE P 80 TYR 0.030 0.002 TYR P 32 ARG 0.011 0.001 ARG P 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 637 time to evaluate : 2.715 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 outliers start: 1 outliers final: 1 residues processed: 637 average time/residue: 0.5950 time to fit residues: 623.8748 Evaluate side-chains 489 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 2.712 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4474 time to fit residues: 3.8387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 383 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 290 optimal weight: 0.6980 chunk 224 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 396 optimal weight: 20.0000 chunk 247 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN G 122 HIS I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS K 26 ASN L 75 HIS ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS R 63 GLN ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN X 97 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 60102 Z= 0.178 Angle : 0.701 14.612 89072 Z= 0.366 Chirality : 0.036 0.329 11163 Planarity : 0.006 0.124 5332 Dihedral : 24.606 177.986 27547 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.73 % Favored : 92.69 % Rotamer: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2584 helix: 0.11 (0.16), residues: 960 sheet: -0.63 (0.26), residues: 399 loop : -2.02 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 24 HIS 0.011 0.001 HIS K 116 PHE 0.020 0.002 PHE B 55 TYR 0.025 0.002 TYR L 69 ARG 0.014 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 664 time to evaluate : 3.109 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 outliers start: 1 outliers final: 0 residues processed: 665 average time/residue: 0.6223 time to fit residues: 683.8502 Evaluate side-chains 507 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 2.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 245 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 236 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 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 16 HIS C 123 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS K 26 ASN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 43 HIS ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 60102 Z= 0.275 Angle : 0.741 14.731 89072 Z= 0.386 Chirality : 0.038 0.299 11163 Planarity : 0.007 0.126 5332 Dihedral : 24.588 178.056 27547 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.01 % Favored : 91.45 % Rotamer: Outliers : 0.14 % Allowed : 1.41 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2584 helix: -0.09 (0.16), residues: 961 sheet: -0.94 (0.25), residues: 418 loop : -2.05 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 24 HIS 0.010 0.002 HIS C 69 PHE 0.023 0.002 PHE N 16 TYR 0.026 0.002 TYR P 32 ARG 0.024 0.001 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 637 time to evaluate : 2.658 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 outliers start: 3 outliers final: 2 residues processed: 639 average time/residue: 0.5873 time to fit residues: 621.4792 Evaluate side-chains 496 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 494 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4694 time to fit residues: 4.7608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 360 optimal weight: 1.9990 chunk 379 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 369 optimal weight: 0.3980 chunk 222 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 333 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 367 optimal weight: 7.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 60102 Z= 0.251 Angle : 0.735 14.705 89072 Z= 0.382 Chirality : 0.038 0.276 11163 Planarity : 0.007 0.127 5332 Dihedral : 24.591 178.139 27547 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 31.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.70 % Favored : 91.83 % Rotamer: Outliers : 0.05 % Allowed : 0.82 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2584 helix: -0.18 (0.16), residues: 957 sheet: -0.98 (0.25), residues: 420 loop : -2.01 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 24 HIS 0.010 0.002 HIS H 82 PHE 0.026 0.002 PHE B 55 TYR 0.027 0.002 TYR P 32 ARG 0.009 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 2.722 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 outliers start: 1 outliers final: 0 residues processed: 633 average time/residue: 0.5774 time to fit residues: 602.2817 Evaluate side-chains 490 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 2.637 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 242 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 409 optimal weight: 30.0000 chunk 376 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 199 optimal weight: 0.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** 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 13 HIS ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 HIS L 76 ASN ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN R 63 GLN ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN W 43 HIS ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 60102 Z= 0.294 Angle : 0.762 14.778 89072 Z= 0.395 Chirality : 0.039 0.260 11163 Planarity : 0.007 0.128 5332 Dihedral : 24.607 178.553 27547 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 34.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.98 % Favored : 90.48 % Rotamer: Outliers : 0.14 % Allowed : 0.32 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2584 helix: -0.31 (0.16), residues: 978 sheet: -1.02 (0.25), residues: 424 loop : -2.02 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 24 HIS 0.010 0.002 HIS H 82 PHE 0.023 0.002 PHE G 26 TYR 0.045 0.002 TYR D 68 ARG 0.010 0.001 ARG W 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5168 Ramachandran restraints generated. 2584 Oldfield, 0 Emsley, 2584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 607 time to evaluate : 2.680 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 outliers start: 3 outliers final: 3 residues processed: 609 average time/residue: 0.5791 time to fit residues: 587.4359 Evaluate side-chains 473 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 2.624 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4366 time to fit residues: 5.3655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 258 optimal weight: 4.9990 chunk 347 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 300 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 326 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 335 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS I 58 HIS ** I 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS ** O 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN T 73 HIS ** X 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.049890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.041105 restraints weight = 433762.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.042417 restraints weight = 163233.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043202 restraints weight = 88502.016| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.6126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 60102 Z= 0.199 Angle : 0.721 20.583 89072 Z= 0.373 Chirality : 0.037 0.241 11163 Planarity : 0.006 0.128 5332 Dihedral : 24.552 179.129 27547 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.24 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.70 (0.16), residues: 2584 helix: -0.24 (0.16), residues: 975 sheet: -0.90 (0.25), residues: 423 loop : -1.96 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 24 HIS 0.013 0.002 HIS T 73 PHE 0.032 0.002 PHE J 63 TYR 0.037 0.002 TYR D 68 ARG 0.013 0.001 ARG N 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11077.28 seconds wall clock time: 198 minutes 47.93 seconds (11927.93 seconds total)