Starting phenix.real_space_refine on Mon Mar 11 05:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_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_4076/03_2024/5lmq_4076_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_4076_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmq_4076/03_2024/5lmq_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-dev-5265/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: 24.89, per 1000 atoms: 0.45 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: 26.28 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: 26.21 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: 45.29 Time building geometry restraints manager: 27.99 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: 33186 35.85 - 71.69: 5053 71.69 - 107.54: 627 107.54 - 143.39: 27 143.39 - 179.24: 54 Dihedral angle restraints: 38947 sinusoidal: 31380 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 38944 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: 0.710 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: 6.160 Check model and map are aligned: 0.630 Set scattering table: 0.410 Process input model: 173.970 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.160 ------------------------------------------------------------------------------- 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 : 26.696 179.237 34083 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 : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 HIS cc_start: 0.6023 (OUTLIER) cc_final: 0.5112 (t70) REVERT: B 23 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7074 (tpm170) REVERT: B 76 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: B 78 GLN cc_start: 0.7344 (tt0) cc_final: 0.6932 (tm-30) REVERT: B 94 ASN cc_start: 0.7778 (t0) cc_final: 0.7018 (t0) REVERT: B 129 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: B 136 VAL cc_start: 0.6813 (OUTLIER) cc_final: 0.5361 (t) REVERT: B 178 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7445 (mmt180) REVERT: B 211 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7338 (pt) REVERT: C 10 PHE cc_start: 0.8367 (t80) cc_final: 0.7993 (t80) REVERT: C 111 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7869 (tt) REVERT: C 142 MET cc_start: 0.7786 (mpm) cc_final: 0.6965 (mmm) REVERT: C 167 TRP cc_start: 0.8427 (OUTLIER) cc_final: 0.8095 (t60) REVERT: C 191 THR cc_start: 0.7618 (OUTLIER) cc_final: 0.6696 (m) REVERT: D 12 CYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6733 (m) REVERT: D 61 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.8661 (tptp) REVERT: D 75 PHE cc_start: 0.8983 (t80) cc_final: 0.8155 (t80) REVERT: D 96 LEU cc_start: 0.8815 (tp) cc_final: 0.8528 (tp) REVERT: D 110 PHE cc_start: 0.7711 (m-80) cc_final: 0.7451 (m-80) REVERT: D 144 ASP cc_start: 0.5978 (m-30) cc_final: 0.5468 (m-30) REVERT: D 205 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 20 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7629 (tm-30) REVERT: E 34 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.6827 (p) REVERT: E 36 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7192 (p0) REVERT: E 37 ARG cc_start: 0.7037 (mtt-85) cc_final: 0.6122 (mtt-85) REVERT: E 41 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8091 (m) REVERT: E 80 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8889 (tp) REVERT: E 118 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8637 (mm) REVERT: E 133 TYR cc_start: 0.7836 (m-80) cc_final: 0.7545 (m-80) REVERT: E 136 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6844 (ttm) REVERT: E 142 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8508 (mp) REVERT: F 7 ASN cc_start: 0.7645 (m-40) cc_final: 0.7378 (m-40) REVERT: F 15 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6583 (p0) REVERT: F 19 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8282 (tt) REVERT: F 54 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.6096 (mmtt) REVERT: F 61 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7950 (mp) REVERT: F 63 TYR cc_start: 0.7998 (m-80) cc_final: 0.7648 (m-80) REVERT: F 91 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.8039 (t) REVERT: G 28 ASN cc_start: 0.8931 (m-40) cc_final: 0.8318 (m-40) REVERT: G 45 ASP cc_start: 0.8038 (m-30) cc_final: 0.7365 (m-30) REVERT: G 49 ILE cc_start: 0.8324 (mt) cc_final: 0.8066 (mm) REVERT: G 50 ILE cc_start: 0.8636 (mt) cc_final: 0.8309 (mm) REVERT: G 156 TRP cc_start: 0.5890 (OUTLIER) cc_final: 0.5208 (m-10) REVERT: H 8 ASP cc_start: 0.8137 (t70) cc_final: 0.7532 (t70) REVERT: H 9 MET cc_start: 0.8067 (ttt) cc_final: 0.7456 (tmm) REVERT: H 10 LEU cc_start: 0.8834 (mt) cc_final: 0.8518 (mt) REVERT: H 13 ILE cc_start: 0.9279 (mt) cc_final: 0.8663 (mt) REVERT: H 15 ASN cc_start: 0.9104 (m-40) cc_final: 0.8869 (m110) REVERT: H 20 TYR cc_start: 0.8780 (m-80) cc_final: 0.8119 (m-80) REVERT: H 34 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8197 (tp30) REVERT: H 38 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.7758 (tp) REVERT: H 52 ASP cc_start: 0.7553 (t70) cc_final: 0.7272 (t0) REVERT: H 85 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8269 (tmt-80) REVERT: H 136 GLU cc_start: 0.7499 (tt0) cc_final: 0.7004 (tt0) REVERT: I 3 GLN cc_start: 0.6534 (tt0) cc_final: 0.6083 (tm-30) REVERT: I 26 VAL cc_start: 0.7768 (t) cc_final: 0.7522 (t) REVERT: I 71 SER cc_start: 0.8182 (t) cc_final: 0.7945 (t) REVERT: I 102 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6858 (tt) REVERT: I 127 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7268 (tmtt) REVERT: J 41 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7248 (Cg_endo) REVERT: K 28 THR cc_start: 0.8069 (m) cc_final: 0.7754 (p) REVERT: K 32 ILE cc_start: 0.8596 (mm) cc_final: 0.8329 (mm) REVERT: K 34 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.7848 (p0) REVERT: K 48 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8706 (mp) REVERT: K 84 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.7986 (t) REVERT: K 108 ILE cc_start: 0.8809 (mt) cc_final: 0.8603 (mp) REVERT: L 27 LEU cc_start: 0.8416 (tp) cc_final: 0.8193 (tp) REVERT: L 82 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8413 (p) REVERT: L 97 ARG cc_start: 0.8803 (mtt-85) cc_final: 0.8510 (mtt180) REVERT: M 22 ILE cc_start: 0.8666 (mt) cc_final: 0.8259 (mp) REVERT: M 23 TYR cc_start: 0.8058 (t80) cc_final: 0.7514 (t80) REVERT: O 8 LYS cc_start: 0.8485 (tttt) cc_final: 0.8230 (tttt) REVERT: O 59 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: O 60 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8392 (p) REVERT: O 65 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: O 87 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7722 (tp) REVERT: P 3 LYS cc_start: 0.8143 (mttt) cc_final: 0.7920 (mtmt) REVERT: P 12 LYS cc_start: 0.8995 (tttt) cc_final: 0.8777 (mtpt) REVERT: P 28 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8874 (ptt-90) REVERT: P 35 LYS cc_start: 0.9284 (tttt) cc_final: 0.9030 (tttp) REVERT: P 38 TYR cc_start: 0.7846 (p90) cc_final: 0.7091 (p90) REVERT: P 40 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8818 (t0) REVERT: P 44 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8836 (p) REVERT: P 49 LEU cc_start: 0.8605 (tp) cc_final: 0.8297 (tt) REVERT: P 65 GLN cc_start: 0.8076 (tp40) cc_final: 0.7813 (tp40) REVERT: Q 7 THR cc_start: 0.8587 (m) cc_final: 0.7019 (p) REVERT: Q 18 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8708 (m) REVERT: Q 20 THR cc_start: 0.8407 (m) cc_final: 0.8187 (p) REVERT: Q 71 PHE cc_start: 0.8554 (m-80) cc_final: 0.8351 (m-10) REVERT: Q 90 ILE cc_start: 0.9116 (mt) cc_final: 0.8560 (mm) REVERT: R 47 THR cc_start: 0.8982 (m) cc_final: 0.8382 (p) REVERT: R 70 ILE cc_start: 0.9251 (mt) cc_final: 0.9048 (mt) REVERT: S 23 ASN cc_start: 0.7190 (m-40) cc_final: 0.6623 (m110) REVERT: S 63 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7039 (m) REVERT: T 18 GLN cc_start: 0.8157 (tt0) cc_final: 0.7877 (tt0) REVERT: T 42 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8224 (mm-40) REVERT: T 72 LEU cc_start: 0.8200 (mt) cc_final: 0.7927 (mp) REVERT: T 74 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7393 (ptpt) REVERT: W 7 ILE cc_start: 0.7565 (mt) cc_final: 0.7247 (mm) REVERT: X 29 MET cc_start: 0.4136 (mmm) cc_final: 0.3888 (mmm) REVERT: X 41 MET cc_start: 0.7544 (mmm) cc_final: 0.6573 (mmm) REVERT: X 62 TYR cc_start: 0.4257 (t80) cc_final: 0.4014 (t80) REVERT: X 122 PHE cc_start: 0.8370 (m-80) cc_final: 0.7947 (m-80) REVERT: X 143 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7871 (t70) outliers start: 473 outliers final: 117 residues processed: 1237 average time/residue: 0.6938 time to fit residues: 1343.0842 Evaluate side-chains 841 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 679 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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: 0.7980 chunk 313 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 240 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS B 25 ASN B 110 GLN B 140 HIS B 212 GLN C 31 HIS C 107 GLN C 108 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 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 7 ASN ** 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** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN I 58 HIS ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 60232 Z= 0.269 Angle : 0.843 15.211 89271 Z= 0.440 Chirality : 0.044 0.313 11185 Planarity : 0.007 0.121 5345 Dihedral : 25.636 178.584 28576 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.96 % Allowed : 8.30 % Favored : 90.74 % Rotamer: Outliers : 0.23 % Allowed : 5.31 % Favored : 94.46 % 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: -1.27 (0.16), residues: 2591 helix: 1.30 (0.17), residues: 988 sheet: -1.48 (0.23), residues: 415 loop : -2.56 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 24 HIS 0.009 0.001 HIS K 116 PHE 0.024 0.003 PHE I 18 TYR 0.030 0.003 TYR E 60 ARG 0.016 0.001 ARG K 18 *********************** 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 904 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 899 time to evaluate : 2.807 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: B 92 TYR cc_start: 0.8393 (p90) cc_final: 0.8159 (p90) REVERT: B 94 ASN cc_start: 0.7654 (t0) cc_final: 0.7326 (t0) REVERT: B 148 TYR cc_start: 0.6798 (m-80) cc_final: 0.6423 (m-80) REVERT: B 193 ASP cc_start: 0.6761 (t0) cc_final: 0.6355 (t0) REVERT: B 206 ASP cc_start: 0.5947 (t0) cc_final: 0.5498 (t0) REVERT: C 56 ASP cc_start: 0.7650 (m-30) cc_final: 0.6771 (m-30) REVERT: D 205 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7415 (mt-10) REVERT: E 20 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7733 (tp-100) REVERT: E 60 TYR cc_start: 0.7344 (t80) cc_final: 0.6814 (t80) REVERT: E 118 ILE cc_start: 0.8997 (pt) cc_final: 0.8404 (mm) REVERT: E 151 LEU cc_start: 0.8407 (mt) cc_final: 0.8119 (mt) REVERT: F 15 ASP cc_start: 0.6486 (p0) cc_final: 0.6191 (p0) REVERT: F 71 ARG cc_start: 0.6960 (mtm180) cc_final: 0.6723 (mmm-85) REVERT: G 26 PHE cc_start: 0.8024 (t80) cc_final: 0.7809 (t80) REVERT: G 49 ILE cc_start: 0.8357 (mt) cc_final: 0.7967 (mm) REVERT: G 101 LEU cc_start: 0.8715 (mt) cc_final: 0.8285 (mt) REVERT: G 105 VAL cc_start: 0.8766 (t) cc_final: 0.8481 (t) REVERT: G 110 GLN cc_start: 0.7740 (mm110) cc_final: 0.7538 (mm-40) REVERT: G 148 ASN cc_start: 0.7045 (p0) cc_final: 0.6700 (p0) REVERT: H 8 ASP cc_start: 0.7847 (t70) cc_final: 0.7548 (t0) REVERT: H 9 MET cc_start: 0.8223 (ttp) cc_final: 0.7717 (tmm) REVERT: H 13 ILE cc_start: 0.9245 (mt) cc_final: 0.8397 (mt) REVERT: H 20 TYR cc_start: 0.8509 (m-80) cc_final: 0.8175 (m-80) REVERT: H 38 ILE cc_start: 0.8954 (mm) cc_final: 0.8715 (mm) REVERT: I 7 THR cc_start: 0.7006 (t) cc_final: 0.6805 (t) REVERT: I 85 LEU cc_start: 0.7588 (mp) cc_final: 0.7343 (mm) REVERT: J 15 THR cc_start: 0.9162 (p) cc_final: 0.8939 (p) REVERT: J 63 PHE cc_start: 0.8107 (m-80) cc_final: 0.7720 (m-80) REVERT: K 11 LYS cc_start: 0.5908 (pttm) cc_final: 0.5643 (pptt) REVERT: K 67 ASP cc_start: 0.8297 (t70) cc_final: 0.7998 (t0) REVERT: L 77 LEU cc_start: 0.8531 (mm) cc_final: 0.8284 (mm) REVERT: L 110 VAL cc_start: 0.8562 (t) cc_final: 0.8357 (t) REVERT: O 7 GLU cc_start: 0.7864 (pt0) cc_final: 0.7543 (pt0) REVERT: P 12 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8419 (mtmt) REVERT: P 34 GLU cc_start: 0.7756 (tt0) cc_final: 0.7445 (tt0) REVERT: P 35 LYS cc_start: 0.9242 (tttt) cc_final: 0.8931 (ttmm) REVERT: P 38 TYR cc_start: 0.7334 (p90) cc_final: 0.6966 (p90) REVERT: P 59 TRP cc_start: 0.8781 (m100) cc_final: 0.8337 (m100) REVERT: P 65 GLN cc_start: 0.8257 (tp40) cc_final: 0.8032 (tp40) REVERT: P 73 LEU cc_start: 0.8718 (mm) cc_final: 0.8321 (mm) REVERT: Q 37 LYS cc_start: 0.7744 (mmmm) cc_final: 0.7391 (mtpp) REVERT: Q 48 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7439 (mt-10) REVERT: Q 76 LEU cc_start: 0.9140 (tp) cc_final: 0.8673 (tp) REVERT: Q 90 ILE cc_start: 0.9156 (mt) cc_final: 0.8889 (mm) REVERT: R 47 THR cc_start: 0.8903 (m) cc_final: 0.8562 (p) REVERT: S 23 ASN cc_start: 0.6647 (m-40) cc_final: 0.6332 (m-40) REVERT: S 44 MET cc_start: 0.7104 (tpp) cc_final: 0.6714 (tpt) REVERT: T 90 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7822 (pp30) REVERT: W 21 THR cc_start: 0.8316 (m) cc_final: 0.7993 (p) REVERT: W 45 ILE cc_start: 0.8314 (mp) cc_final: 0.7582 (tp) REVERT: W 46 ARG cc_start: 0.7079 (mtm180) cc_final: 0.6647 (mtm-85) REVERT: X 164 LEU cc_start: 0.8274 (tt) cc_final: 0.7944 (tt) outliers start: 5 outliers final: 0 residues processed: 900 average time/residue: 0.6344 time to fit residues: 904.4515 Evaluate side-chains 644 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 2.819 ------------------------------------------------------------------------------- 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: 10.0000 chunk 116 optimal weight: 9.9990 chunk 312 optimal weight: 20.0000 chunk 255 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 375 optimal weight: 8.9990 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: 2.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS J 78 ASN K 26 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN T 18 GLN X 15 GLN X 97 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4431 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= 0.336 Angle : 0.814 14.234 89271 Z= 0.426 Chirality : 0.042 0.294 11185 Planarity : 0.007 0.118 5345 Dihedral : 25.562 178.541 28576 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 31.55 Ramachandran Plot: Outliers : 0.89 % Allowed : 9.38 % Favored : 89.73 % Rotamer: Outliers : 0.32 % Allowed : 6.13 % Favored : 93.56 % 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: -1.29 (0.17), residues: 2591 helix: 0.99 (0.16), residues: 967 sheet: -1.50 (0.24), residues: 434 loop : -2.22 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 24 HIS 0.014 0.002 HIS J 56 PHE 0.022 0.003 PHE B 17 TYR 0.030 0.002 TYR F 63 ARG 0.007 0.001 ARG R 53 *********************** 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 762 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 755 time to evaluate : 2.854 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: B 25 ASN cc_start: 0.8411 (t0) cc_final: 0.8147 (t0) REVERT: B 193 ASP cc_start: 0.6594 (t0) cc_final: 0.6367 (t0) REVERT: D 205 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7524 (mt-10) REVERT: E 47 LYS cc_start: 0.8343 (mttt) cc_final: 0.7740 (mtpt) REVERT: E 118 ILE cc_start: 0.8986 (pt) cc_final: 0.8520 (mm) REVERT: F 15 ASP cc_start: 0.6119 (p0) cc_final: 0.5910 (p0) REVERT: G 26 PHE cc_start: 0.8016 (t80) cc_final: 0.7772 (t80) REVERT: G 28 ASN cc_start: 0.8919 (m-40) cc_final: 0.8284 (m-40) REVERT: G 31 MET cc_start: 0.8611 (ttm) cc_final: 0.8312 (ttt) REVERT: G 101 LEU cc_start: 0.8556 (mt) cc_final: 0.8264 (mp) REVERT: G 110 GLN cc_start: 0.7763 (mm110) cc_final: 0.7546 (mm-40) REVERT: G 148 ASN cc_start: 0.7016 (p0) cc_final: 0.6716 (p0) REVERT: H 1 MET cc_start: 0.7396 (ttm) cc_final: 0.7039 (ttm) REVERT: H 8 ASP cc_start: 0.8254 (t70) cc_final: 0.7539 (t0) REVERT: H 9 MET cc_start: 0.8111 (ttp) cc_final: 0.7846 (tmm) REVERT: H 13 ILE cc_start: 0.9281 (mt) cc_final: 0.8785 (mt) REVERT: H 17 THR cc_start: 0.9215 (p) cc_final: 0.8332 (p) REVERT: H 20 TYR cc_start: 0.8801 (m-80) cc_final: 0.8214 (m-80) REVERT: H 121 ASP cc_start: 0.7667 (p0) cc_final: 0.7439 (p0) REVERT: I 85 LEU cc_start: 0.8119 (mp) cc_final: 0.7852 (mm) REVERT: K 50 TYR cc_start: 0.5689 (m-10) cc_final: 0.5351 (m-10) REVERT: L 77 LEU cc_start: 0.8267 (mm) cc_final: 0.8031 (mm) REVERT: L 93 LEU cc_start: 0.8980 (mt) cc_final: 0.8381 (mt) REVERT: M 120 LYS cc_start: 0.3273 (pttm) cc_final: 0.2824 (mmtt) REVERT: N 45 ARG cc_start: 0.8284 (ttt-90) cc_final: 0.7949 (ttt-90) REVERT: O 11 VAL cc_start: 0.8835 (t) cc_final: 0.8359 (t) REVERT: O 71 GLN cc_start: 0.8134 (tp40) cc_final: 0.7932 (tp-100) REVERT: P 12 LYS cc_start: 0.8908 (ttmt) cc_final: 0.8610 (mtmt) REVERT: P 35 LYS cc_start: 0.9394 (tttt) cc_final: 0.9185 (tttp) REVERT: P 38 TYR cc_start: 0.7409 (p90) cc_final: 0.6396 (p90) REVERT: P 49 LEU cc_start: 0.8735 (tt) cc_final: 0.7687 (tt) REVERT: P 73 LEU cc_start: 0.8895 (mm) cc_final: 0.8620 (tt) REVERT: Q 12 SER cc_start: 0.7756 (t) cc_final: 0.7374 (p) REVERT: R 47 THR cc_start: 0.9080 (m) cc_final: 0.8801 (p) REVERT: S 11 VAL cc_start: 0.7575 (t) cc_final: 0.7363 (t) REVERT: W 9 THR cc_start: 0.7840 (p) cc_final: 0.7630 (p) REVERT: W 45 ILE cc_start: 0.8523 (mp) cc_final: 0.7734 (tp) REVERT: X 122 PHE cc_start: 0.8060 (m-10) cc_final: 0.7844 (m-80) outliers start: 7 outliers final: 2 residues processed: 757 average time/residue: 0.6003 time to fit residues: 732.7474 Evaluate side-chains 589 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 587 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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: 10.0000 chunk 282 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 chunk 252 optimal weight: 7.9990 chunk 377 optimal weight: 4.9990 chunk 399 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 HIS B 240 GLN C 108 ASN C 136 GLN F 7 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 HIS J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN S 23 ASN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 18 GLN ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4889 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= 0.246 Angle : 0.737 13.665 89271 Z= 0.388 Chirality : 0.039 0.290 11185 Planarity : 0.007 0.118 5345 Dihedral : 25.377 179.759 28576 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.26 % Favored : 91.01 % Rotamer: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.23 % 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: -1.16 (0.17), residues: 2591 helix: 0.86 (0.16), residues: 972 sheet: -1.37 (0.25), residues: 437 loop : -1.95 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 97 HIS 0.009 0.001 HIS T 73 PHE 0.022 0.002 PHE B 57 TYR 0.023 0.002 TYR I 5 ARG 0.036 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 763 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 759 time to evaluate : 2.944 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: B 25 ASN cc_start: 0.8340 (t0) cc_final: 0.7919 (t0) REVERT: B 148 TYR cc_start: 0.6888 (m-80) cc_final: 0.6614 (m-80) REVERT: B 152 PHE cc_start: 0.7640 (t80) cc_final: 0.7408 (t80) REVERT: B 179 LYS cc_start: 0.7368 (ttmt) cc_final: 0.6992 (tttt) REVERT: B 189 ASP cc_start: 0.6819 (p0) cc_final: 0.6414 (p0) REVERT: D 68 TYR cc_start: 0.7597 (m-80) cc_final: 0.7375 (m-10) REVERT: D 190 ASP cc_start: 0.6492 (t70) cc_final: 0.6030 (t0) REVERT: D 205 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7394 (mt-10) REVERT: E 11 ILE cc_start: 0.9031 (mp) cc_final: 0.8544 (mp) REVERT: E 47 LYS cc_start: 0.8280 (mttt) cc_final: 0.8069 (mttt) REVERT: E 136 MET cc_start: 0.6650 (tpp) cc_final: 0.6086 (tpp) REVERT: G 26 PHE cc_start: 0.7740 (t80) cc_final: 0.7517 (t80) REVERT: G 28 ASN cc_start: 0.8776 (m-40) cc_final: 0.8322 (m-40) REVERT: G 31 MET cc_start: 0.8802 (ttm) cc_final: 0.8465 (ttp) REVERT: G 101 LEU cc_start: 0.8570 (mt) cc_final: 0.8354 (mt) REVERT: G 106 GLN cc_start: 0.7649 (pp30) cc_final: 0.7334 (pp30) REVERT: H 1 MET cc_start: 0.7435 (ttm) cc_final: 0.6854 (ttm) REVERT: H 8 ASP cc_start: 0.8411 (t70) cc_final: 0.7446 (t0) REVERT: H 9 MET cc_start: 0.8106 (ttp) cc_final: 0.7636 (tmm) REVERT: H 13 ILE cc_start: 0.9235 (mt) cc_final: 0.8712 (mt) REVERT: H 20 TYR cc_start: 0.8686 (m-80) cc_final: 0.8158 (m-80) REVERT: J 48 THR cc_start: 0.7724 (m) cc_final: 0.7497 (p) REVERT: K 124 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7895 (ptmt) REVERT: L 6 THR cc_start: 0.8412 (t) cc_final: 0.7892 (m) REVERT: L 65 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8325 (mm-30) REVERT: L 122 THR cc_start: 0.8476 (m) cc_final: 0.8237 (m) REVERT: N 49 HIS cc_start: 0.7703 (m-70) cc_final: 0.7270 (m-70) REVERT: O 11 VAL cc_start: 0.8871 (t) cc_final: 0.8337 (t) REVERT: O 71 GLN cc_start: 0.8230 (tp40) cc_final: 0.7966 (tp-100) REVERT: P 12 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8595 (ttmt) REVERT: P 34 GLU cc_start: 0.7791 (tt0) cc_final: 0.7436 (tt0) REVERT: P 38 TYR cc_start: 0.7236 (p90) cc_final: 0.6180 (p90) REVERT: Q 6 LEU cc_start: 0.8826 (mp) cc_final: 0.8542 (mm) REVERT: R 47 THR cc_start: 0.9018 (m) cc_final: 0.8393 (p) REVERT: S 63 THR cc_start: 0.7419 (m) cc_final: 0.7096 (m) REVERT: W 9 THR cc_start: 0.7768 (p) cc_final: 0.7547 (p) REVERT: W 21 THR cc_start: 0.8451 (m) cc_final: 0.8051 (p) REVERT: W 45 ILE cc_start: 0.8509 (mp) cc_final: 0.7790 (tp) REVERT: X 122 PHE cc_start: 0.7767 (m-10) cc_final: 0.7542 (m-80) outliers start: 4 outliers final: 0 residues processed: 760 average time/residue: 0.5834 time to fit residues: 722.1942 Evaluate side-chains 597 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 2.818 ------------------------------------------------------------------------------- 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: 8.9990 chunk 226 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 340 optimal weight: 0.9990 chunk 275 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 B 140 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS I 124 GLN J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 GLN ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 60232 Z= 0.265 Angle : 0.740 13.639 89271 Z= 0.390 Chirality : 0.039 0.300 11185 Planarity : 0.006 0.117 5345 Dihedral : 25.322 179.630 28576 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.49 % Favored : 90.89 % Rotamer: Outliers : 0.18 % Allowed : 3.31 % Favored : 96.51 % 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: -1.22 (0.17), residues: 2591 helix: 0.71 (0.16), residues: 977 sheet: -1.39 (0.25), residues: 437 loop : -1.89 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP G 103 HIS 0.013 0.001 HIS X 114 PHE 0.017 0.002 PHE J 47 TYR 0.019 0.002 TYR O 78 ARG 0.008 0.001 ARG N 19 *********************** 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 722 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 718 time to evaluate : 2.832 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: B 148 TYR cc_start: 0.6915 (m-80) cc_final: 0.6668 (m-80) REVERT: B 155 LEU cc_start: 0.7400 (mt) cc_final: 0.7154 (mt) REVERT: D 190 ASP cc_start: 0.6714 (t70) cc_final: 0.6341 (t70) REVERT: D 205 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 90 VAL cc_start: 0.8563 (p) cc_final: 0.7993 (p) REVERT: E 118 ILE cc_start: 0.8691 (pt) cc_final: 0.8073 (mm) REVERT: E 136 MET cc_start: 0.6717 (tpp) cc_final: 0.6499 (tpp) REVERT: E 151 LEU cc_start: 0.8810 (mt) cc_final: 0.8605 (mt) REVERT: F 74 ASP cc_start: 0.6428 (t0) cc_final: 0.6162 (t0) REVERT: G 28 ASN cc_start: 0.8804 (m-40) cc_final: 0.8325 (m-40) REVERT: G 31 MET cc_start: 0.8737 (ttm) cc_final: 0.8329 (ttp) REVERT: G 101 LEU cc_start: 0.8838 (mt) cc_final: 0.8409 (mt) REVERT: H 8 ASP cc_start: 0.8372 (t70) cc_final: 0.7444 (t0) REVERT: H 9 MET cc_start: 0.8122 (ttp) cc_final: 0.7740 (tmm) REVERT: H 13 ILE cc_start: 0.9251 (mt) cc_final: 0.8715 (mt) REVERT: H 20 TYR cc_start: 0.8712 (m-80) cc_final: 0.8198 (m-80) REVERT: H 81 HIS cc_start: 0.7633 (m90) cc_final: 0.7116 (m90) REVERT: I 5 TYR cc_start: 0.5229 (t80) cc_final: 0.4819 (t80) REVERT: J 19 SER cc_start: 0.9045 (m) cc_final: 0.8598 (m) REVERT: L 77 LEU cc_start: 0.8320 (mm) cc_final: 0.8082 (mm) REVERT: N 49 HIS cc_start: 0.7708 (m-70) cc_final: 0.7336 (m-70) REVERT: O 11 VAL cc_start: 0.8835 (t) cc_final: 0.8352 (t) REVERT: O 13 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7919 (pp30) REVERT: O 15 PHE cc_start: 0.7401 (m-80) cc_final: 0.6886 (m-80) REVERT: O 83 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: P 12 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8632 (ttmt) REVERT: P 34 GLU cc_start: 0.7709 (tt0) cc_final: 0.7426 (tt0) REVERT: P 35 LYS cc_start: 0.9244 (tttt) cc_final: 0.8990 (ttmm) REVERT: P 38 TYR cc_start: 0.7344 (p90) cc_final: 0.6505 (p90) REVERT: P 49 LEU cc_start: 0.8899 (tt) cc_final: 0.8177 (tt) REVERT: P 76 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8145 (tm-30) REVERT: W 9 THR cc_start: 0.7891 (p) cc_final: 0.7658 (p) REVERT: X 83 THR cc_start: 0.5794 (p) cc_final: 0.5522 (p) REVERT: X 122 PHE cc_start: 0.7809 (m-10) cc_final: 0.7518 (m-80) outliers start: 4 outliers final: 0 residues processed: 720 average time/residue: 0.5737 time to fit residues: 677.1662 Evaluate side-chains 576 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 574 time to evaluate : 2.807 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 136 GLN E 141 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 49 ASN R 63 GLN T 18 GLN T 73 HIS ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5556 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= 0.313 Angle : 0.774 13.484 89271 Z= 0.406 Chirality : 0.040 0.338 11185 Planarity : 0.007 0.117 5345 Dihedral : 25.360 179.790 28576 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 31.80 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.95 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -1.42 (0.17), residues: 2591 helix: 0.42 (0.16), residues: 985 sheet: -1.49 (0.24), residues: 433 loop : -1.91 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.004 TRP G 103 HIS 0.032 0.002 HIS X 114 PHE 0.019 0.002 PHE D 79 TYR 0.031 0.002 TYR X 99 ARG 0.010 0.001 ARG E 140 *********************** 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 706 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 706 time to evaluate : 2.849 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: B 25 ASN cc_start: 0.8213 (t0) cc_final: 0.7995 (t0) REVERT: B 102 LEU cc_start: 0.8693 (mt) cc_final: 0.8329 (mm) REVERT: B 146 GLN cc_start: 0.5664 (pp30) cc_final: 0.4935 (pp30) REVERT: B 148 TYR cc_start: 0.6955 (m-80) cc_final: 0.6701 (m-80) REVERT: D 205 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7486 (mt-10) REVERT: E 90 VAL cc_start: 0.8564 (p) cc_final: 0.7987 (p) REVERT: E 118 ILE cc_start: 0.8810 (pt) cc_final: 0.8145 (mm) REVERT: E 130 ASN cc_start: 0.8411 (m110) cc_final: 0.8014 (m110) REVERT: E 141 GLN cc_start: 0.6879 (tp40) cc_final: 0.6617 (tp-100) REVERT: F 24 GLU cc_start: 0.7218 (tp30) cc_final: 0.6420 (tp30) REVERT: G 28 ASN cc_start: 0.8814 (m110) cc_final: 0.8178 (m-40) REVERT: G 31 MET cc_start: 0.8769 (ttm) cc_final: 0.8311 (ttp) REVERT: G 122 HIS cc_start: 0.7131 (m-70) cc_final: 0.6831 (m90) REVERT: H 8 ASP cc_start: 0.8471 (t70) cc_final: 0.7475 (t0) REVERT: H 9 MET cc_start: 0.8015 (ttp) cc_final: 0.7789 (tmm) REVERT: H 20 TYR cc_start: 0.8714 (m-80) cc_final: 0.8240 (m-80) REVERT: H 38 ILE cc_start: 0.9132 (mm) cc_final: 0.8858 (mm) REVERT: H 81 HIS cc_start: 0.7475 (m90) cc_final: 0.7152 (m90) REVERT: I 70 LYS cc_start: 0.7445 (mptt) cc_final: 0.7190 (mmtt) REVERT: I 112 LYS cc_start: 0.8203 (tptp) cc_final: 0.7918 (tptt) REVERT: I 124 GLN cc_start: 0.8878 (pt0) cc_final: 0.8643 (pt0) REVERT: L 122 THR cc_start: 0.8410 (m) cc_final: 0.8208 (m) REVERT: M 82 MET cc_start: 0.6787 (mmm) cc_final: 0.6529 (mmm) REVERT: N 9 LYS cc_start: 0.6783 (mmtt) cc_final: 0.6159 (mmtp) REVERT: N 22 THR cc_start: 0.8717 (p) cc_final: 0.8457 (p) REVERT: N 49 HIS cc_start: 0.7690 (m-70) cc_final: 0.7017 (m-70) REVERT: O 11 VAL cc_start: 0.8897 (t) cc_final: 0.8291 (t) REVERT: O 14 GLU cc_start: 0.7935 (pp20) cc_final: 0.7325 (pp20) REVERT: O 15 PHE cc_start: 0.7582 (m-80) cc_final: 0.6867 (m-80) REVERT: P 12 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8672 (ttmt) REVERT: P 34 GLU cc_start: 0.7778 (tt0) cc_final: 0.7449 (tt0) REVERT: P 35 LYS cc_start: 0.9211 (tttt) cc_final: 0.8950 (ttmm) REVERT: P 38 TYR cc_start: 0.7528 (p90) cc_final: 0.7109 (p90) REVERT: P 47 ASP cc_start: 0.8011 (t0) cc_final: 0.7563 (t0) REVERT: Q 23 VAL cc_start: 0.9488 (t) cc_final: 0.9236 (p) REVERT: R 81 PHE cc_start: 0.8414 (t80) cc_final: 0.7549 (t80) REVERT: W 21 THR cc_start: 0.8424 (m) cc_final: 0.7989 (p) outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.5913 time to fit residues: 691.9288 Evaluate side-chains 551 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 2.824 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 336 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 113 HIS C 108 ASN C 136 GLN G 13 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 106 GLN G 122 HIS ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 HIS H 82 HIS ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** 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 L 49 ASN R 63 GLN T 18 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 60232 Z= 0.225 Angle : 0.711 13.447 89271 Z= 0.376 Chirality : 0.037 0.301 11185 Planarity : 0.006 0.117 5345 Dihedral : 25.222 179.313 28576 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 26.69 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.53 % Favored : 91.82 % Rotamer: Outliers : 0.05 % Allowed : 2.22 % Favored : 97.73 % 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: 0.63 (0.17), residues: 982 sheet: -1.30 (0.25), residues: 422 loop : -1.89 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP G 103 HIS 0.027 0.002 HIS X 114 PHE 0.027 0.002 PHE X 122 TYR 0.026 0.002 TYR D 207 ARG 0.009 0.001 ARG W 8 *********************** 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 701 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 700 time to evaluate : 2.878 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: B 148 TYR cc_start: 0.6805 (m-80) cc_final: 0.6590 (m-80) REVERT: B 157 ARG cc_start: 0.7333 (mpt90) cc_final: 0.7020 (mmt-90) REVERT: C 26 LYS cc_start: 0.7096 (tmmt) cc_final: 0.6781 (ttpt) REVERT: D 103 ASN cc_start: 0.7826 (t0) cc_final: 0.7492 (t0) REVERT: D 205 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 90 VAL cc_start: 0.8516 (p) cc_final: 0.7919 (p) REVERT: E 118 ILE cc_start: 0.8745 (pt) cc_final: 0.8161 (mm) REVERT: E 130 ASN cc_start: 0.8215 (m110) cc_final: 0.7841 (m110) REVERT: E 142 LEU cc_start: 0.9288 (mt) cc_final: 0.9050 (mp) REVERT: G 28 ASN cc_start: 0.8677 (m110) cc_final: 0.8125 (m-40) REVERT: G 31 MET cc_start: 0.8730 (ttm) cc_final: 0.8127 (ttp) REVERT: G 96 GLN cc_start: 0.8034 (tt0) cc_final: 0.6835 (tt0) REVERT: G 99 LEU cc_start: 0.8320 (mm) cc_final: 0.7162 (mm) REVERT: G 101 LEU cc_start: 0.8529 (mt) cc_final: 0.8228 (mt) REVERT: G 102 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7456 (ttm110) REVERT: G 106 GLN cc_start: 0.7204 (pt0) cc_final: 0.6679 (pt0) REVERT: G 122 HIS cc_start: 0.7172 (m90) cc_final: 0.6874 (m90) REVERT: H 8 ASP cc_start: 0.8546 (t70) cc_final: 0.7800 (t70) REVERT: H 20 TYR cc_start: 0.8828 (m-80) cc_final: 0.8291 (m-80) REVERT: H 81 HIS cc_start: 0.7273 (m-70) cc_final: 0.6977 (m-70) REVERT: I 5 TYR cc_start: 0.5237 (t80) cc_final: 0.4940 (t80) REVERT: I 11 LYS cc_start: 0.8501 (ttmt) cc_final: 0.8184 (mttt) REVERT: I 112 LYS cc_start: 0.8100 (tptp) cc_final: 0.7860 (tptp) REVERT: I 116 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7797 (mmmm) REVERT: I 124 GLN cc_start: 0.8641 (pt0) cc_final: 0.8300 (pt0) REVERT: J 56 HIS cc_start: 0.8192 (m170) cc_final: 0.7865 (m170) REVERT: L 77 LEU cc_start: 0.8348 (mm) cc_final: 0.8085 (mm) REVERT: L 122 THR cc_start: 0.8309 (m) cc_final: 0.8102 (m) REVERT: M 4 ILE cc_start: 0.6730 (mm) cc_final: 0.6483 (mm) REVERT: M 82 MET cc_start: 0.6970 (mmm) cc_final: 0.6747 (mmm) REVERT: M 120 LYS cc_start: 0.4172 (pttm) cc_final: 0.3439 (mmtt) REVERT: N 49 HIS cc_start: 0.7554 (m-70) cc_final: 0.7130 (m-70) REVERT: O 11 VAL cc_start: 0.8867 (t) cc_final: 0.8375 (t) REVERT: O 14 GLU cc_start: 0.8020 (pp20) cc_final: 0.7715 (pp20) REVERT: P 12 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8625 (ttmt) REVERT: P 35 LYS cc_start: 0.9028 (tttt) cc_final: 0.8741 (ttmm) REVERT: P 38 TYR cc_start: 0.7354 (p90) cc_final: 0.6932 (p90) REVERT: P 47 ASP cc_start: 0.7885 (t0) cc_final: 0.7342 (t0) REVERT: P 49 LEU cc_start: 0.8543 (tp) cc_final: 0.8321 (tt) REVERT: Q 83 ASP cc_start: 0.7614 (p0) cc_final: 0.7166 (p0) REVERT: W 21 THR cc_start: 0.8438 (m) cc_final: 0.8130 (p) REVERT: X 161 MET cc_start: 0.5480 (tpt) cc_final: 0.5214 (tpt) outliers start: 1 outliers final: 0 residues processed: 700 average time/residue: 0.5697 time to fit residues: 662.0157 Evaluate side-chains 570 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 2.921 ------------------------------------------------------------------------------- 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: 4.9990 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 253 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 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 16 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN H 81 HIS H 82 HIS ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN L 49 ASN R 63 GLN T 18 GLN T 73 HIS ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 60232 Z= 0.364 Angle : 0.820 25.795 89271 Z= 0.426 Chirality : 0.042 0.318 11185 Planarity : 0.007 0.194 5345 Dihedral : 25.392 178.534 28576 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 35.78 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.57 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -1.65 (0.16), residues: 2591 helix: 0.12 (0.16), residues: 997 sheet: -1.44 (0.24), residues: 436 loop : -2.02 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP C 167 HIS 0.027 0.002 HIS X 114 PHE 0.027 0.002 PHE R 81 TYR 0.032 0.003 TYR C 23 ARG 0.010 0.001 ARG E 126 *********************** 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 675 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 675 time to evaluate : 2.873 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: B 113 HIS cc_start: 0.6900 (t70) cc_final: 0.6325 (t-170) REVERT: B 146 GLN cc_start: 0.5337 (pp30) cc_final: 0.4760 (pp30) REVERT: C 26 LYS cc_start: 0.7275 (tmmt) cc_final: 0.6879 (ttpt) REVERT: D 67 ILE cc_start: 0.8518 (mt) cc_final: 0.8295 (mt) REVERT: D 103 ASN cc_start: 0.7909 (t0) cc_final: 0.7614 (t0) REVERT: D 190 ASP cc_start: 0.7206 (t70) cc_final: 0.6820 (t0) REVERT: E 47 LYS cc_start: 0.8202 (mttt) cc_final: 0.7677 (mtpt) REVERT: E 127 ASN cc_start: 0.8710 (t0) cc_final: 0.8498 (t0) REVERT: E 130 ASN cc_start: 0.8074 (m110) cc_final: 0.7765 (m110) REVERT: G 28 ASN cc_start: 0.8781 (m110) cc_final: 0.8244 (m-40) REVERT: G 31 MET cc_start: 0.8828 (ttm) cc_final: 0.8419 (ttp) REVERT: G 101 LEU cc_start: 0.8769 (mt) cc_final: 0.8366 (mt) REVERT: G 122 HIS cc_start: 0.7014 (m90) cc_final: 0.6669 (m-70) REVERT: H 2 LEU cc_start: 0.8460 (mm) cc_final: 0.8146 (mm) REVERT: H 8 ASP cc_start: 0.8376 (t70) cc_final: 0.7404 (t0) REVERT: H 119 LEU cc_start: 0.8777 (pp) cc_final: 0.8523 (pp) REVERT: I 5 TYR cc_start: 0.5568 (t80) cc_final: 0.5174 (t80) REVERT: I 112 LYS cc_start: 0.8269 (tptp) cc_final: 0.7961 (tptp) REVERT: I 124 GLN cc_start: 0.8839 (pt0) cc_final: 0.8505 (pt0) REVERT: M 82 MET cc_start: 0.7027 (mmm) cc_final: 0.6821 (mmm) REVERT: N 49 HIS cc_start: 0.7648 (m-70) cc_final: 0.7138 (m-70) REVERT: N 52 GLN cc_start: 0.8753 (pm20) cc_final: 0.8497 (pm20) REVERT: O 14 GLU cc_start: 0.8095 (pp20) cc_final: 0.7764 (pp20) REVERT: P 12 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8615 (ttmt) REVERT: P 34 GLU cc_start: 0.7613 (tt0) cc_final: 0.7399 (tt0) REVERT: P 38 TYR cc_start: 0.7358 (p90) cc_final: 0.6891 (p90) REVERT: P 47 ASP cc_start: 0.7949 (t0) cc_final: 0.7431 (t0) REVERT: Q 83 ASP cc_start: 0.7757 (p0) cc_final: 0.7373 (p0) REVERT: R 33 ASP cc_start: 0.7825 (t0) cc_final: 0.7594 (m-30) REVERT: W 21 THR cc_start: 0.8489 (m) cc_final: 0.8139 (p) outliers start: 0 outliers final: 0 residues processed: 675 average time/residue: 0.5944 time to fit residues: 668.3045 Evaluate side-chains 529 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 2.804 ------------------------------------------------------------------------------- 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: 10.0000 chunk 381 optimal weight: 0.0060 chunk 347 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 291 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 335 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS B 40 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 49 ASN O 28 GLN R 63 GLN T 18 GLN T 73 HIS ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.6152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 60232 Z= 0.200 Angle : 0.705 13.326 89271 Z= 0.373 Chirality : 0.037 0.293 11185 Planarity : 0.006 0.118 5345 Dihedral : 25.178 179.722 28576 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 25.36 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.06 % Favored : 92.40 % Rotamer: Outliers : 0.09 % Allowed : 1.09 % Favored : 98.82 % 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: -1.32 (0.17), residues: 2591 helix: 0.47 (0.16), residues: 987 sheet: -1.20 (0.25), residues: 416 loop : -1.92 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP G 103 HIS 0.021 0.001 HIS X 114 PHE 0.023 0.002 PHE Q 71 TYR 0.028 0.002 TYR D 207 ARG 0.014 0.001 ARG D 209 *********************** 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 696 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 694 time to evaluate : 2.814 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: B 146 GLN cc_start: 0.5248 (pp30) cc_final: 0.4676 (pp30) REVERT: C 6 HIS cc_start: 0.8215 (t-170) cc_final: 0.7876 (t-170) REVERT: C 8 ILE cc_start: 0.9460 (mm) cc_final: 0.9047 (mm) REVERT: C 26 LYS cc_start: 0.7134 (tmmt) cc_final: 0.6816 (ttpt) REVERT: D 67 ILE cc_start: 0.8375 (mt) cc_final: 0.8126 (mt) REVERT: D 103 ASN cc_start: 0.7937 (t0) cc_final: 0.7594 (t0) REVERT: D 190 ASP cc_start: 0.6934 (t70) cc_final: 0.6634 (t0) REVERT: D 205 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7257 (mt-10) REVERT: E 47 LYS cc_start: 0.8209 (mttt) cc_final: 0.7734 (mtpt) REVERT: E 118 ILE cc_start: 0.8722 (pt) cc_final: 0.8160 (mm) REVERT: G 31 MET cc_start: 0.8694 (ttm) cc_final: 0.8373 (ttp) REVERT: G 99 LEU cc_start: 0.8377 (mm) cc_final: 0.6991 (mm) REVERT: G 101 LEU cc_start: 0.8521 (mt) cc_final: 0.8299 (mt) REVERT: G 102 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7462 (ttm110) REVERT: G 122 HIS cc_start: 0.6930 (m90) cc_final: 0.6574 (m-70) REVERT: H 8 ASP cc_start: 0.8501 (t70) cc_final: 0.7645 (t0) REVERT: H 15 ASN cc_start: 0.8945 (m-40) cc_final: 0.8733 (m-40) REVERT: H 119 LEU cc_start: 0.8652 (pp) cc_final: 0.8429 (pp) REVERT: I 5 TYR cc_start: 0.5636 (t80) cc_final: 0.5322 (t80) REVERT: I 112 LYS cc_start: 0.7895 (tptp) cc_final: 0.7680 (tptp) REVERT: I 116 LYS cc_start: 0.8286 (mmmm) cc_final: 0.7908 (mmmm) REVERT: I 124 GLN cc_start: 0.8629 (pt0) cc_final: 0.8324 (pt0) REVERT: J 56 HIS cc_start: 0.8268 (m170) cc_final: 0.7849 (m170) REVERT: L 122 THR cc_start: 0.8267 (m) cc_final: 0.8023 (m) REVERT: M 120 LYS cc_start: 0.3835 (pttm) cc_final: 0.3407 (mmtt) REVERT: N 45 ARG cc_start: 0.8230 (ttt-90) cc_final: 0.7957 (ttt-90) REVERT: N 46 GLU cc_start: 0.6782 (tm-30) cc_final: 0.5636 (tm-30) REVERT: N 49 HIS cc_start: 0.7634 (m-70) cc_final: 0.7013 (m-70) REVERT: N 52 GLN cc_start: 0.8884 (pm20) cc_final: 0.8338 (pm20) REVERT: O 14 GLU cc_start: 0.7978 (pp20) cc_final: 0.7740 (pp20) REVERT: P 12 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8632 (ttmt) REVERT: P 34 GLU cc_start: 0.7096 (tt0) cc_final: 0.6808 (tt0) REVERT: P 38 TYR cc_start: 0.7293 (p90) cc_final: 0.6971 (p90) REVERT: P 47 ASP cc_start: 0.8058 (t0) cc_final: 0.7535 (t0) REVERT: Q 83 ASP cc_start: 0.7753 (p0) cc_final: 0.7469 (p0) REVERT: W 21 THR cc_start: 0.8511 (m) cc_final: 0.8256 (p) REVERT: W 63 THR cc_start: 0.8783 (m) cc_final: 0.8568 (t) REVERT: W 69 TYR cc_start: 0.6094 (t80) cc_final: 0.5641 (t80) REVERT: X 29 MET cc_start: 0.3459 (ptp) cc_final: 0.2897 (mtm) outliers start: 2 outliers final: 0 residues processed: 695 average time/residue: 0.5617 time to fit residues: 649.6293 Evaluate side-chains 551 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 551 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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: 6.9990 chunk 392 optimal weight: 8.9990 chunk 239 optimal weight: 0.2980 chunk 186 optimal weight: 8.9990 chunk 272 optimal weight: 30.0000 chunk 411 optimal weight: 30.0000 chunk 378 optimal weight: 8.9990 chunk 327 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 253 optimal weight: 0.0170 chunk 200 optimal weight: 3.9990 overall best weight: 2.3222 ------------------------------------------------------------------------------- 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** C 108 ASN C 136 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 106 GLN H 82 HIS ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 GLN L 49 ASN R 63 GLN T 18 GLN ** X 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 60232 Z= 0.181 Angle : 0.690 13.333 89271 Z= 0.364 Chirality : 0.036 0.291 11185 Planarity : 0.006 0.117 5345 Dihedral : 25.033 178.809 28576 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.53 % Favored : 91.97 % Rotamer: Outliers : 0.05 % Allowed : 0.54 % Favored : 99.41 % 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: -1.24 (0.17), residues: 2591 helix: 0.45 (0.16), residues: 991 sheet: -1.19 (0.25), residues: 419 loop : -1.79 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 97 HIS 0.022 0.001 HIS X 114 PHE 0.035 0.002 PHE G 43 TYR 0.021 0.002 TYR C 23 ARG 0.009 0.001 ARG N 29 ********************** 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 701 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 700 time to evaluate : 2.795 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: B 146 GLN cc_start: 0.5066 (pp30) cc_final: 0.4626 (pp30) REVERT: C 8 ILE cc_start: 0.9449 (mm) cc_final: 0.9017 (mm) REVERT: D 67 ILE cc_start: 0.8280 (mt) cc_final: 0.8057 (mt) REVERT: D 205 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7538 (mt-10) REVERT: E 47 LYS cc_start: 0.8235 (mttt) cc_final: 0.7916 (mtpt) REVERT: E 142 LEU cc_start: 0.9209 (mt) cc_final: 0.8977 (mp) REVERT: G 31 MET cc_start: 0.8632 (ttm) cc_final: 0.8386 (ttp) REVERT: G 98 SER cc_start: 0.8385 (p) cc_final: 0.7816 (p) REVERT: G 99 LEU cc_start: 0.8371 (mm) cc_final: 0.7122 (mm) REVERT: G 102 ARG cc_start: 0.8236 (ttm110) cc_final: 0.7444 (ttm110) REVERT: H 1 MET cc_start: 0.7608 (ppp) cc_final: 0.7061 (ttp) REVERT: H 8 ASP cc_start: 0.8257 (t70) cc_final: 0.7344 (t0) REVERT: H 15 ASN cc_start: 0.8845 (m-40) cc_final: 0.8636 (m-40) REVERT: H 52 ASP cc_start: 0.7372 (t0) cc_final: 0.7083 (t0) REVERT: I 5 TYR cc_start: 0.5431 (t80) cc_final: 0.5032 (t80) REVERT: J 56 HIS cc_start: 0.8200 (m170) cc_final: 0.7827 (m170) REVERT: L 122 THR cc_start: 0.8162 (m) cc_final: 0.7954 (m) REVERT: M 69 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6326 (tm-30) REVERT: M 120 LYS cc_start: 0.3659 (pttm) cc_final: 0.3438 (mmtt) REVERT: N 42 ILE cc_start: 0.8412 (tt) cc_final: 0.8187 (tt) REVERT: N 49 HIS cc_start: 0.7257 (m-70) cc_final: 0.6985 (m-70) REVERT: N 50 LYS cc_start: 0.9037 (mtmt) cc_final: 0.8724 (mttp) REVERT: O 14 GLU cc_start: 0.8046 (pp20) cc_final: 0.7777 (pp20) REVERT: P 12 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8538 (ttmt) REVERT: P 38 TYR cc_start: 0.7221 (p90) cc_final: 0.7002 (p90) REVERT: P 47 ASP cc_start: 0.7899 (t0) cc_final: 0.7423 (t0) REVERT: Q 83 ASP cc_start: 0.7755 (p0) cc_final: 0.7438 (p0) REVERT: Q 90 ILE cc_start: 0.9156 (mm) cc_final: 0.8667 (tt) REVERT: V 13 ILE cc_start: 0.9075 (tt) cc_final: 0.8847 (tt) REVERT: W 21 THR cc_start: 0.8552 (m) cc_final: 0.8312 (p) REVERT: W 63 THR cc_start: 0.8733 (m) cc_final: 0.8410 (t) REVERT: X 83 THR cc_start: 0.5956 (p) cc_final: 0.5738 (p) REVERT: X 114 HIS cc_start: 0.6563 (m-70) cc_final: 0.6188 (m-70) outliers start: 1 outliers final: 0 residues processed: 700 average time/residue: 0.5635 time to fit residues: 655.2008 Evaluate side-chains 554 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 2.811 ------------------------------------------------------------------------------- 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: 6.9990 chunk 349 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 chunk 302 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 336 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN H 82 HIS ** I 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN R 63 GLN T 18 GLN T 73 HIS ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 97 HIS ** 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 = 0.3278 r_free = 0.3278 target = 0.053419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.043485 restraints weight = 375649.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.044749 restraints weight = 141056.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.045523 restraints weight = 78432.737| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 60232 Z= 0.333 Angle : 0.779 13.277 89271 Z= 0.407 Chirality : 0.040 0.317 11185 Planarity : 0.007 0.118 5345 Dihedral : 25.232 179.632 28576 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 33.51 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.95 % Favored : 90.58 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % 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: -1.44 (0.16), residues: 2591 helix: 0.24 (0.16), residues: 975 sheet: -1.08 (0.26), residues: 402 loop : -1.92 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP G 103 HIS 0.024 0.002 HIS X 114 PHE 0.026 0.002 PHE R 81 TYR 0.020 0.002 TYR B 31 ARG 0.013 0.001 ARG Q 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11652.55 seconds wall clock time: 207 minutes 20.23 seconds (12440.23 seconds total)