Starting phenix.real_space_refine on Fri Dec 8 06:32:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/12_2023/5lmq_4076_neut_updated.pdb" } resolution = 4.2 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= 0.023 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 1607 5.49 5 Mg 64 5.21 5 S 61 5.16 5 C 28740 2.51 5 N 10510 2.21 5 O 14857 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 20": "OE1" <-> "OE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" 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 145": "OE1" <-> "OE2" 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 200": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "F GLU 5": "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 "F GLU 69": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 77": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H GLU 136": "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 "J GLU 95": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 48": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q GLU 86": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "X GLU 4": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 131": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 55841 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 32522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1514, 32522 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "', 'pdbres=" A A 914 "', 'pdbres=" C A1397 "'] Classifications: {'RNA': 1514} Modifications used: {'5*END': 4, 'rna2p_pur': 104, 'rna2p_pyr': 72, 'rna3p_pur': 751, 'rna3p_pyr': 587} Link IDs: {'rna2p': 176, 'rna3p': 1337} 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: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 906 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} 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: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 459 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 16} Chain: "Z" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 2, 'rna3p': 5, 'rna3p_pur': 29, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 66} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Unusual residues: {' MG': 63} Classifications: {'undetermined': 63} Link IDs: {None: 62} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36093 SG CYS D 9 85.637 102.827 147.902 1.00 50.00 S ATOM 36236 SG CYS D 26 82.873 104.575 148.176 1.00 50.00 S ATOM 36276 SG CYS D 31 84.757 105.897 147.095 1.00 50.00 S ATOM 46965 SG CYS N 24 153.779 118.698 134.617 1.00 50.00 S ATOM 46989 SG CYS N 27 152.221 115.875 133.675 1.00 50.00 S ATOM 47121 SG CYS N 43 150.074 118.735 132.795 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: 22.30, per 1000 atoms: 0.40 Number of scatterers: 55841 At special positions: 0 Unit cell: (227.8, 183.58, 205.02, 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 1607 15.00 Mg 64 11.99 O 14857 8.00 N 10510 7.00 C 28740 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: 25.70 Conformation dependent library (CDL) restraints added in 3.2 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 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 23 sheets defined 33.9% alpha, 15.2% beta 522 base pairs and 914 stacking pairs defined. Time for finding SS restraints: 24.82 Creating SS restraints... Processing helix chain 'B' and resid 46 through 63 Processing helix chain 'B' and resid 80 through 87 Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.878A pdb=" N GLN B 110 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 134 through 145 removed outlier: 3.630A pdb=" N LYS B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.921A pdb=" N ILE B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.685A pdb=" N LEU C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' 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 91 through 98 Processing helix chain 'D' and resid 101 through 107 Processing helix chain 'D' and resid 114 through 122 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 156 through 165 Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'E' and resid 51 through 64 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.966A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 109 " --> pdb=" O VAL E 105 " (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 17 through 33 Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.651A pdb=" N ASN F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 4.208A pdb=" N ARG G 41 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 129 Processing helix chain 'G' and resid 134 through 144 Processing helix chain 'G' and resid 151 through 153 No H-bonds generated for 'chain 'G' and resid 151 through 153' Processing helix chain 'H' and resid 6 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 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 48 through 53 Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'J' and resid 13 through 27 removed outlier: 3.748A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'K' and resid 53 through 56 removed outlier: 3.599A pdb=" N GLY K 56 " --> pdb=" O SER K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 56' Processing helix chain 'K' and resid 58 through 75 removed outlier: 3.941A pdb=" N TYR K 75 " --> pdb=" O LYS K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 101 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 28 through 37 Processing helix chain 'M' and resid 50 through 63 removed outlier: 3.600A pdb=" N ASN M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 83 Processing helix chain 'M' and resid 87 through 94 Processing helix chain 'M' and resid 108 through 111 No H-bonds generated for 'chain 'M' and resid 108 through 111' Processing helix chain 'N' and resid 41 through 50 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.616A pdb=" N VAL O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 77 Processing helix chain 'Q' and resid 82 through 97 removed outlier: 3.759A pdb=" N LYS Q 87 " --> pdb=" O ASP Q 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 25 No H-bonds generated for 'chain 'R' and resid 22 through 25' Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 16 through 20 Processing helix chain 'T' and resid 14 through 46 Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 74 through 93 removed outlier: 3.827A pdb=" N ALA T 78 " --> pdb=" O LYS T 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 15 Processing helix chain 'W' and resid 18 through 20 No H-bonds generated for 'chain 'W' and resid 18 through 20' 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 81 removed outlier: 3.737A pdb=" N LYS X 81 " --> pdb=" O ARG X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 126 through 143 Proline residue: X 130 - end of helix removed outlier: 3.958A pdb=" N ARG X 139 " --> pdb=" O ARG X 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 68 through 71 removed outlier: 6.883A pdb=" N ALA B 161 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 71 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE B 163 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 199 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 188 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILE B 201 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 32 through 36 removed outlier: 6.975A pdb=" N ILE B 41 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.731A pdb=" N GLN C 104 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.609A 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 removed outlier: 3.668A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY C 197 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= F, first strand: chain 'E' and resid 66 through 68 removed outlier: 6.247A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 80 through 84 removed outlier: 3.616A pdb=" N LYS E 88 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.061A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 73 through 79 Processing sheet with id= J, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= K, first strand: chain 'H' and resid 82 through 85 removed outlier: 6.905A pdb=" N ILE H 111 " --> pdb=" O ILE H 134 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU H 136 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE H 109 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 3 through 10 Processing sheet with id= M, first strand: chain 'J' and resid 68 through 74 removed outlier: 3.618A pdb=" N VAL J 72 " --> pdb=" O ILE J 6 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 39 through 44 removed outlier: 6.787A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER K 44 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR K 28 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG K 85 " --> pdb=" O ALA K 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 82 through 85 removed outlier: 6.791A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG L 53 " --> pdb=" O THR L 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'P' and resid 2 through 8 removed outlier: 6.184A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Q' and resid 71 through 73 removed outlier: 14.319A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.328A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 56 through 58 removed outlier: 3.507A pdb=" N GLU Q 78 " --> pdb=" O VAL Q 56 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 48 through 52 Processing sheet with id= T, first strand: chain 'W' and resid 7 through 12 removed outlier: 8.641A pdb=" N GLY W 65 " --> pdb=" O GLU W 31 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU W 33 " --> pdb=" O GLY W 65 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE W 67 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR W 35 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE W 32 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL W 24 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG W 23 " --> pdb=" O GLU W 15 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS W 25 " --> pdb=" O VAL W 13 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N VAL W 13 " --> pdb=" O LYS W 25 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 15 through 18 removed outlier: 4.093A pdb=" N GLY X 27 " --> pdb=" O VAL X 18 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 85 through 91 removed outlier: 6.223A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'X' and resid 44 through 49 removed outlier: 7.172A pdb=" N VAL X 56 " --> pdb=" O VAL X 48 " (cutoff:3.500A) 769 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1397 hydrogen bonds 2392 hydrogen bond angles 0 basepair planarities 522 basepair parallelities 914 stacking parallelities Total time for adding SS restraints: 43.26 Time building geometry restraints manager: 27.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7090 1.33 - 1.45: 25344 1.45 - 1.58: 24493 1.58 - 1.70: 3198 1.70 - 1.82: 107 Bond restraints: 60232 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.491 0.311 2.00e-02 2.50e+03 2.41e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.361 0.274 2.00e-02 2.50e+03 1.88e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.394 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.344 -0.162 2.00e-02 2.50e+03 6.60e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.358 0.140 2.00e-02 2.50e+03 4.92e+01 ... (remaining 60227 not shown) Histogram of bond angle deviations from ideal: 83.74 - 94.60: 2 94.60 - 105.46: 8176 105.46 - 116.31: 44038 116.31 - 127.17: 33281 127.17 - 138.03: 3774 Bond angle restraints: 89271 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 109.46 83.74 25.72 1.66e+00 3.63e-01 2.40e+02 angle pdb=" O3' G A 575 " pdb=" C3' G A 575 " pdb=" C2' G A 575 " ideal model delta sigma weight residual 109.50 127.07 -17.57 1.50e+00 4.44e-01 1.37e+02 angle pdb=" N ILE C 14 " pdb=" CA ILE C 14 " pdb=" C ILE C 14 " ideal model delta sigma weight residual 110.42 121.45 -11.03 9.60e-01 1.09e+00 1.32e+02 angle pdb=" O3' U A1301 " pdb=" C3' U A1301 " pdb=" C2' U A1301 " ideal model delta sigma weight residual 109.50 125.52 -16.02 1.50e+00 4.44e-01 1.14e+02 angle pdb=" C ARG W 23 " pdb=" CA ARG W 23 " pdb=" CB ARG W 23 " ideal model delta sigma weight residual 109.80 93.02 16.78 1.64e+00 3.72e-01 1.05e+02 ... (remaining 89266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 32643 35.85 - 71.69: 4614 71.69 - 107.54: 627 107.54 - 143.39: 27 143.39 - 179.24: 54 Dihedral angle restraints: 37965 sinusoidal: 30398 harmonic: 7567 Sorted by residual: dihedral pdb=" C ARG W 23 " pdb=" N ARG W 23 " pdb=" CA ARG W 23 " pdb=" CB ARG W 23 " ideal model delta harmonic sigma weight residual -122.60 -91.01 -31.59 0 2.50e+00 1.60e-01 1.60e+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 67.59 79.41 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' U A 992 " pdb=" C4' U A 992 " pdb=" C3' U A 992 " pdb=" O3' U A 992 " ideal model delta sinusoidal sigma weight residual 147.00 71.50 75.50 1 8.00e+00 1.56e-02 1.12e+02 ... (remaining 37962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 10358 0.220 - 0.440: 770 0.440 - 0.660: 29 0.660 - 0.880: 23 0.880 - 1.101: 5 Chirality restraints: 11185 Sorted by residual: chirality pdb=" C3' G A 575 " pdb=" C4' G A 575 " pdb=" O3' G A 575 " pdb=" C2' G A 575 " both_signs ideal model delta sigma weight residual False -2.74 -1.64 -1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" C3' G A 181 " pdb=" C4' G A 181 " pdb=" O3' G A 181 " pdb=" C2' G A 181 " both_signs ideal model delta sigma weight residual False -2.74 -1.70 -1.04 2.00e-01 2.50e+01 2.71e+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 -1.76 -0.99 2.00e-01 2.50e+01 2.45e+01 ... (remaining 11182 not shown) Planarity restraints: 5345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU Z 54 " 0.068 2.00e-02 2.50e+03 5.52e-01 6.85e+03 pdb=" C4' 5MU Z 54 " -0.465 2.00e-02 2.50e+03 pdb=" O4' 5MU Z 54 " -0.751 2.00e-02 2.50e+03 pdb=" C3' 5MU Z 54 " 0.542 2.00e-02 2.50e+03 pdb=" O3' 5MU Z 54 " 0.478 2.00e-02 2.50e+03 pdb=" C2' 5MU Z 54 " 0.240 2.00e-02 2.50e+03 pdb=" O2' 5MU Z 54 " -0.747 2.00e-02 2.50e+03 pdb=" C1' 5MU Z 54 " -0.238 2.00e-02 2.50e+03 pdb=" N1 5MU Z 54 " 0.872 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4SU Z 8 " -0.125 2.00e-02 2.50e+03 5.31e-01 6.34e+03 pdb=" C4' 4SU Z 8 " 0.458 2.00e-02 2.50e+03 pdb=" O4' 4SU Z 8 " 0.835 2.00e-02 2.50e+03 pdb=" C3' 4SU Z 8 " -0.534 2.00e-02 2.50e+03 pdb=" O3' 4SU Z 8 " -0.373 2.00e-02 2.50e+03 pdb=" C2' 4SU Z 8 " -0.293 2.00e-02 2.50e+03 pdb=" O2' 4SU Z 8 " 0.637 2.00e-02 2.50e+03 pdb=" C1' 4SU Z 8 " 0.205 2.00e-02 2.50e+03 pdb=" N1 4SU Z 8 " -0.809 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC Z 32 " 0.071 2.00e-02 2.50e+03 5.09e-01 5.84e+03 pdb=" C4' OMC Z 32 " -0.476 2.00e-02 2.50e+03 pdb=" O4' OMC Z 32 " -0.579 2.00e-02 2.50e+03 pdb=" C3' OMC Z 32 " 0.512 2.00e-02 2.50e+03 pdb=" O3' OMC Z 32 " 0.449 2.00e-02 2.50e+03 pdb=" C2' OMC Z 32 " 0.247 2.00e-02 2.50e+03 pdb=" O2' OMC Z 32 " -0.770 2.00e-02 2.50e+03 pdb=" C1' OMC Z 32 " -0.227 2.00e-02 2.50e+03 pdb=" N1 OMC Z 32 " 0.775 2.00e-02 2.50e+03 ... (remaining 5342 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 42 2.09 - 2.79: 10733 2.79 - 3.49: 82869 3.49 - 4.20: 185310 4.20 - 4.90: 242011 Nonbonded interactions: 520965 Sorted by model distance: nonbonded pdb=" OP2 A A 439 " pdb=" N2 G A 493 " model vdw 1.387 2.520 nonbonded pdb=" OP1 A A 782 " pdb="MG MG A1625 " model vdw 1.392 2.170 nonbonded pdb=" OP2 A A 768 " pdb="MG MG A1623 " model vdw 1.435 2.170 nonbonded pdb=" OP1 G A 426 " pdb=" NH1 ARG D 36 " model vdw 1.445 2.520 nonbonded pdb=" OP2 C A 596 " pdb="MG MG A1627 " model vdw 1.484 2.170 ... (remaining 520960 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 6.060 Check model and map are aligned: 0.640 Set scattering table: 0.430 Process input model: 165.190 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.130 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: 176.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.311 60232 Z= 0.540 Angle : 1.443 25.716 89271 Z= 0.964 Chirality : 0.121 1.101 11185 Planarity : 0.017 0.552 5345 Dihedral : 26.296 179.237 33101 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 3.43 % Allowed : 10.50 % Favored : 86.07 % Rotamer: Outliers : 21.46 % Allowed : 18.38 % Favored : 60.16 % Cbeta Deviations : 1.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % Twisted General : 0.16 % 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: -2.56 (0.14), residues: 2591 helix: 0.15 (0.14), residues: 986 sheet: -2.03 (0.23), residues: 411 loop : -3.29 (0.15), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 138 HIS 0.010 0.002 HIS L 75 PHE 0.022 0.003 PHE G 62 TYR 0.029 0.003 TYR O 78 ARG 0.025 0.002 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1452 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 473 poor density : 979 time to evaluate : 2.837 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: 473 outliers final: 117 residues processed: 1237 average time/residue: 0.6997 time to fit residues: 1347.1611 Evaluate side-chains 790 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 673 time to evaluate : 2.783 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 2 residues processed: 117 average time/residue: 0.6818 time to fit residues: 129.8436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 348 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 110 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN C 31 HIS C 107 GLN C 108 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS D 129 ASN D 201 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN S 83 HIS T 73 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 60232 Z= 0.293 Angle : 0.854 14.470 89271 Z= 0.449 Chirality : 0.045 0.319 11185 Planarity : 0.007 0.121 5345 Dihedral : 25.142 179.191 27594 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.07 % Favored : 89.97 % Rotamer: Outliers : 0.54 % Allowed : 6.94 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.74 % 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: -1.42 (0.16), residues: 2591 helix: 1.09 (0.16), residues: 994 sheet: -1.54 (0.23), residues: 429 loop : -2.61 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 24 HIS 0.013 0.001 HIS B 16 PHE 0.029 0.003 PHE Q 71 TYR 0.024 0.003 TYR E 60 ARG 0.011 0.001 ARG N 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 847 time to evaluate : 2.918 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 outliers start: 12 outliers final: 3 residues processed: 852 average time/residue: 0.6337 time to fit residues: 858.9428 Evaluate side-chains 623 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 620 time to evaluate : 2.789 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3993 time to fit residues: 5.3422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 208 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 50.0000 chunk 255 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 375 optimal weight: 2.9990 chunk 405 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 301 optimal weight: 0.0470 overall best weight: 3.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 HIS ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN J 13 HIS J 78 ASN K 26 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN T 18 GLN ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 GLN X 97 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 60232 Z= 0.222 Angle : 0.740 13.947 89271 Z= 0.392 Chirality : 0.039 0.266 11185 Planarity : 0.007 0.118 5345 Dihedral : 24.797 179.929 27594 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.72 % Favored : 90.39 % Rotamer: Outliers : 0.27 % Allowed : 5.26 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2591 helix: 1.28 (0.17), residues: 965 sheet: -1.14 (0.25), residues: 420 loop : -2.15 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 24 HIS 0.011 0.001 HIS J 56 PHE 0.024 0.002 PHE Q 71 TYR 0.031 0.002 TYR K 25 ARG 0.012 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 788 time to evaluate : 3.290 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 outliers start: 6 outliers final: 0 residues processed: 790 average time/residue: 0.6249 time to fit residues: 795.6235 Evaluate side-chains 591 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 371 optimal weight: 6.9990 chunk 282 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 252 optimal weight: 6.9990 chunk 377 optimal weight: 7.9990 chunk 399 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 HIS C 107 GLN C 108 ASN ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN F 7 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN ** O 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 HIS ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 60232 Z= 0.272 Angle : 0.748 13.842 89271 Z= 0.394 Chirality : 0.039 0.287 11185 Planarity : 0.007 0.118 5345 Dihedral : 24.786 179.689 27594 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.81 % Allowed : 8.07 % Favored : 91.12 % Rotamer: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.17), residues: 2591 helix: 0.96 (0.16), residues: 971 sheet: -1.21 (0.24), residues: 437 loop : -1.98 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 97 HIS 0.007 0.001 HIS J 68 PHE 0.022 0.002 PHE B 57 TYR 0.021 0.002 TYR B 199 ARG 0.018 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 721 time to evaluate : 2.999 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 outliers start: 4 outliers final: 0 residues processed: 722 average time/residue: 0.6040 time to fit residues: 710.8319 Evaluate side-chains 572 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 572 time to evaluate : 2.820 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 332 optimal weight: 7.9990 chunk 226 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 275 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 0.4980 chunk 358 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN E 141 GLN F 7 ASN F 18 GLN G 28 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN R 63 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN T 73 HIS ** T 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 60232 Z= 0.291 Angle : 0.759 13.596 89271 Z= 0.399 Chirality : 0.039 0.294 11185 Planarity : 0.007 0.118 5345 Dihedral : 24.809 179.882 27594 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.22 % Favored : 91.12 % Rotamer: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % 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: -1.23 (0.17), residues: 2591 helix: 0.64 (0.16), residues: 974 sheet: -1.19 (0.24), residues: 439 loop : -1.92 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP S 34 HIS 0.008 0.002 HIS D 43 PHE 0.021 0.002 PHE E 26 TYR 0.023 0.002 TYR O 78 ARG 0.008 0.001 ARG E 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 708 time to evaluate : 2.992 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 outliers start: 2 outliers final: 0 residues processed: 709 average time/residue: 0.6272 time to fit residues: 728.4857 Evaluate side-chains 546 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 2.724 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 134 optimal weight: 10.0000 chunk 359 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 331 optimal weight: 5.9990 chunk 185 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN F 7 ASN ** F 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN K 27 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN R 63 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN X 69 GLN ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 60232 Z= 0.264 Angle : 0.739 13.504 89271 Z= 0.389 Chirality : 0.038 0.295 11185 Planarity : 0.006 0.117 5345 Dihedral : 24.756 179.949 27594 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 28.49 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.07 % Favored : 91.28 % Rotamer: Outliers : 0.09 % Allowed : 2.99 % Favored : 96.91 % 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: -1.23 (0.17), residues: 2591 helix: 0.59 (0.16), residues: 977 sheet: -1.27 (0.24), residues: 441 loop : -1.85 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP C 167 HIS 0.014 0.002 HIS X 114 PHE 0.020 0.002 PHE Q 71 TYR 0.023 0.002 TYR O 78 ARG 0.008 0.001 ARG Q 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 714 time to evaluate : 2.804 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 outliers start: 2 outliers final: 0 residues processed: 715 average time/residue: 0.6040 time to fit residues: 705.7033 Evaluate side-chains 553 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 553 time to evaluate : 2.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 385 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 227 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 226 optimal weight: 0.0770 chunk 336 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 overall best weight: 3.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 113 HIS B 140 HIS C 107 GLN C 108 ASN C 118 GLN C 136 GLN E 141 GLN F 18 GLN G 122 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS J 78 ASN K 13 GLN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 8 ASN R 63 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN T 73 HIS W 43 HIS ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 60232 Z= 0.205 Angle : 0.706 22.721 89271 Z= 0.371 Chirality : 0.037 0.287 11185 Planarity : 0.006 0.184 5345 Dihedral : 24.631 179.279 27594 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 25.11 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.62 % Rotamer: Outliers : 0.18 % Allowed : 2.18 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -1.11 (0.17), residues: 2591 helix: 0.71 (0.17), residues: 979 sheet: -1.11 (0.24), residues: 429 loop : -1.85 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 103 HIS 0.015 0.002 HIS X 114 PHE 0.026 0.002 PHE J 54 TYR 0.035 0.002 TYR I 5 ARG 0.008 0.001 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 710 time to evaluate : 2.825 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 outliers start: 4 outliers final: 1 residues processed: 711 average time/residue: 0.6226 time to fit residues: 725.6093 Evaluate side-chains 549 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 548 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4678 time to fit residues: 3.9490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 246 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN F 7 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 78 ASN ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 49 ASN O 28 GLN O 53 HIS R 63 GLN T 18 GLN ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 60232 Z= 0.363 Angle : 0.817 13.346 89271 Z= 0.426 Chirality : 0.042 0.319 11185 Planarity : 0.007 0.118 5345 Dihedral : 24.849 179.879 27594 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 36.15 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.61 % Favored : 89.81 % Rotamer: Outliers : 0.05 % Allowed : 1.54 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -1.50 (0.16), residues: 2591 helix: 0.20 (0.16), residues: 989 sheet: -1.24 (0.25), residues: 436 loop : -1.94 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP C 167 HIS 0.013 0.002 HIS K 116 PHE 0.026 0.003 PHE E 26 TYR 0.036 0.003 TYR C 23 ARG 0.011 0.001 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 680 time to evaluate : 2.916 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 outliers start: 1 outliers final: 1 residues processed: 681 average time/residue: 0.5942 time to fit residues: 663.8310 Evaluate side-chains 523 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.815 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4816 time to fit residues: 3.9581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 362 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 335 optimal weight: 1.9990 chunk 350 optimal weight: 0.6980 chunk 369 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN C 69 HIS C 107 GLN C 108 ASN C 136 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 49 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 HIS R 63 GLN S 23 ASN T 18 GLN T 73 HIS ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 60232 Z= 0.228 Angle : 0.727 13.354 89271 Z= 0.382 Chirality : 0.038 0.300 11185 Planarity : 0.006 0.117 5345 Dihedral : 24.702 179.368 27594 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 27.38 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.99 % Favored : 91.47 % Rotamer: Outliers : 0.14 % Allowed : 0.91 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -1.26 (0.16), residues: 2591 helix: 0.43 (0.16), residues: 968 sheet: -1.01 (0.26), residues: 403 loop : -1.83 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP M 64 HIS 0.016 0.002 HIS J 56 PHE 0.021 0.002 PHE D 79 TYR 0.024 0.002 TYR C 23 ARG 0.009 0.001 ARG L 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 674 time to evaluate : 3.405 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 outliers start: 3 outliers final: 1 residues processed: 675 average time/residue: 0.5971 time to fit residues: 673.3196 Evaluate side-chains 536 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 535 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4685 time to fit residues: 3.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 243 optimal weight: 9.9990 chunk 392 optimal weight: 30.0000 chunk 239 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 411 optimal weight: 30.0000 chunk 378 optimal weight: 7.9990 chunk 327 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN C 69 HIS C 108 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN F 84 ASN G 13 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS K 99 GLN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 49 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN T 18 GLN ** X 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 60232 Z= 0.289 Angle : 0.761 13.286 89271 Z= 0.399 Chirality : 0.039 0.412 11185 Planarity : 0.007 0.118 5345 Dihedral : 24.737 178.606 27594 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 31.86 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.11 % Favored : 90.35 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -1.34 (0.16), residues: 2591 helix: 0.33 (0.16), residues: 966 sheet: -1.03 (0.26), residues: 406 loop : -1.86 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP C 167 HIS 0.010 0.002 HIS K 116 PHE 0.022 0.002 PHE E 26 TYR 0.030 0.002 TYR C 23 ARG 0.011 0.001 ARG H 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5182 Ramachandran restraints generated. 2591 Oldfield, 0 Emsley, 2591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 2.929 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 outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.6003 time to fit residues: 648.4071 Evaluate side-chains 529 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 260 optimal weight: 20.0000 chunk 349 optimal weight: 0.5980 chunk 100 optimal weight: 40.0000 chunk 302 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 328 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS C 107 GLN C 108 ASN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN G 13 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN T 18 GLN T 73 HIS ** X 100 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 = 0.3302 r_free = 0.3302 target = 0.054380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044533 restraints weight = 370647.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.045816 restraints weight = 137680.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046599 restraints weight = 75905.311| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.6399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 60232 Z= 0.250 Angle : 0.734 13.290 89271 Z= 0.386 Chirality : 0.038 0.325 11185 Planarity : 0.006 0.118 5345 Dihedral : 24.690 178.260 27594 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.38 % Favored : 91.16 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.87 % 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: -1.30 (0.16), residues: 2591 helix: 0.34 (0.17), residues: 973 sheet: -0.98 (0.26), residues: 397 loop : -1.82 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 103 HIS 0.009 0.002 HIS B 113 PHE 0.025 0.002 PHE D 79 TYR 0.027 0.002 TYR C 23 ARG 0.011 0.001 ARG H 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11899.81 seconds wall clock time: 212 minutes 51.58 seconds (12771.58 seconds total)