Starting phenix.real_space_refine on Fri Dec 8 03:37:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/12_2023/5lmu_4080_neut_updated.pdb" } resolution = 4.0 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1610 5.49 5 Mg 80 5.21 5 S 59 5.16 5 C 28314 2.51 5 N 10386 2.21 5 O 14744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 9": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C GLU 206": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 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 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 GLU 68": "OE1" <-> "OE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 137": "OE1" <-> "OE2" Residue "E GLU 149": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F GLU 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 52": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 142": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 49": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "I GLU 2": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 128": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 83": "OE1" <-> "OE2" Residue "J GLU 95": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 26": "OE1" <-> "OE2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q GLU 49": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T GLU 93": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X ARG 123": "NH1" <-> "NH2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X GLU 126": "OE1" <-> "OE2" Residue "X GLU 155": "OE1" <-> "OE2" Residue "X ARG 159": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 55195 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 32548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1515, 32548 Inner-chain residues flagged as termini: ['pdbres=" G A 567 "'] Classifications: {'RNA': 1515} Modifications used: {'5*END': 2, 'rna2p_pur': 109, 'rna2p_pyr': 76, 'rna3p_pur': 746, 'rna3p_pyr': 584} Link IDs: {'rna2p': 185, 'rna3p': 1329} Chain breaks: 5 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1900 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 11, 'TRANS': 222} Chain: "C" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "D" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "E" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1146 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "F" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "G" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "H" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "J" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 792 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 970 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "M" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 937 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "N" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "O" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "P" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 700 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "Q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "S" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 655 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "V" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 208 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "X" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1336 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 1 Chain: "Y" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 439 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain breaks: 1 Chain: "Z" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 28} Link IDs: {'rna2p': 11, 'rna3p': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Unusual residues: {' MG': 78} Classifications: {'undetermined': 78} Link IDs: {None: 77} 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: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 36119 SG CYS D 9 86.858 103.754 146.258 1.00 50.00 S ATOM 36262 SG CYS D 26 84.045 105.190 146.650 1.00 50.00 S ATOM 36302 SG CYS D 31 86.251 107.042 145.608 1.00 50.00 S ATOM 46910 SG CYS N 24 149.570 113.831 136.169 1.00 50.00 S ATOM 46934 SG CYS N 27 147.718 111.364 134.822 1.00 50.00 S ATOM 47041 SG CYS N 40 148.804 113.416 131.937 1.00 50.00 S ATOM 47066 SG CYS N 43 146.298 114.571 134.247 1.00 50.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG A1678 " occ=0.63 residue: pdb="ZN ZN N 101 " occ=0.92 Time building chain proxies: 20.68, per 1000 atoms: 0.37 Number of scatterers: 55195 At special positions: 0 Unit cell: (226.46, 180.9, 207.7, 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 59 16.00 P 1610 15.00 Mg 80 11.99 O 14744 8.00 N 10386 7.00 C 28314 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: 24.22 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 24 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 43 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " Number of angles added : 6 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 21 sheets defined 34.4% alpha, 15.0% beta 520 base pairs and 881 stacking pairs defined. Time for finding SS restraints: 25.02 Creating SS restraints... Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.652A pdb=" N ALA B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 145 removed outlier: 6.454A pdb=" N ARG B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 209 through 226 Processing helix chain 'C' and resid 8 through 10 No H-bonds generated for 'chain 'C' and resid 8 through 10' Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 72 through 84 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.595A pdb=" N PHE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) 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 153 Processing helix chain 'D' and resid 156 through 164 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: 3.596A pdb=" N ALA E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 141 Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'F' and resid 16 through 33 Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 69 through 81 removed outlier: 4.363A pdb=" N ASN F 73 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 52 removed outlier: 4.312A 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 removed outlier: 3.551A pdb=" N ILE G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 147 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' Processing helix chain 'H' and resid 5 through 19 Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 103 through 106 Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'I' and resid 33 through 36 No H-bonds generated for 'chain 'I' and resid 33 through 36' Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.823A pdb=" N VAL I 44 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 53 No H-bonds generated for 'chain 'I' and resid 50 through 53' Processing helix chain 'I' and resid 70 through 88 Processing helix chain 'I' and resid 92 through 95 Processing helix chain 'J' and resid 13 through 27 Processing helix chain 'J' and resid 81 through 87 removed outlier: 4.386A pdb=" N MET J 86 " --> pdb=" O ILE J 82 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR J 87 " --> pdb=" O GLU J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 58 through 75 removed outlier: 3.727A 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 12 Processing helix chain 'L' and resid 117 through 120 Processing helix chain 'M' and resid 15 through 21 removed outlier: 3.612A pdb=" N TYR M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 removed outlier: 3.743A pdb=" N LYS M 31 " --> pdb=" O LYS M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 63 removed outlier: 3.595A pdb=" N LEU M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 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 43 through 50 Processing helix chain 'O' and resid 5 through 15 Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 51 through 73 Processing helix chain 'O' and resid 75 through 85 Processing helix chain 'P' and resid 53 through 62 Processing helix chain 'P' and resid 68 through 77 Processing helix chain 'Q' and resid 82 through 98 removed outlier: 3.753A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER Q 97 " --> pdb=" O GLN Q 93 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 40 No H-bonds generated for 'chain 'R' and resid 37 through 40' Processing helix chain 'R' and resid 53 through 56 No H-bonds generated for 'chain 'R' and resid 53 through 56' Processing helix chain 'R' and resid 60 through 76 Processing helix chain 'S' and resid 71 through 73 No H-bonds generated for 'chain 'S' and resid 71 through 73' Processing helix chain 'T' and resid 13 through 46 removed outlier: 3.877A pdb=" N GLU T 46 " --> pdb=" O GLN T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 68 Processing helix chain 'T' and resid 76 through 93 Processing helix chain 'V' and resid 10 through 15 Processing helix chain 'X' and resid 31 through 41 Processing helix chain 'X' and resid 62 through 77 Processing helix chain 'X' and resid 96 through 112 Processing helix chain 'X' and resid 129 through 143 Processing sheet with id= A, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= B, first strand: chain 'C' and resid 55 through 59 removed outlier: 6.896A pdb=" N ASN C 102 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL C 70 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLN C 104 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 164 through 171 Processing sheet with id= D, first strand: chain 'D' and resid 126 through 128 Processing sheet with id= E, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.940A pdb=" N GLN E 20 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 33 " --> pdb=" O MET E 10 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N MET E 10 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY E 35 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU E 8 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 80 through 82 Processing sheet with id= G, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.168A pdb=" N GLY F 44 " --> pdb=" O PHE F 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 73 through 80 Processing sheet with id= I, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= J, first strand: chain 'H' and resid 82 through 85 Processing sheet with id= K, first strand: chain 'I' and resid 3 through 10 Processing sheet with id= L, first strand: chain 'J' and resid 94 through 96 removed outlier: 3.798A pdb=" N GLY J 10 " --> pdb=" O HIS J 68 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 43 through 50 Processing sheet with id= N, first strand: chain 'K' and resid 39 through 43 removed outlier: 6.585A pdb=" N ILE K 32 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TRP K 42 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL K 30 " --> pdb=" O TRP K 42 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N SER K 79 " --> pdb=" O GLY K 17 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA K 19 " --> pdb=" O SER K 79 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP K 81 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE K 21 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE K 83 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA K 23 " --> pdb=" O ILE K 83 " (cutoff:3.500A) removed outlier: 6.831A 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: 6.709A pdb=" N LYS L 57 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N VAL L 40 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL L 55 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR L 42 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 6.087A 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: 6.490A pdb=" N VAL P 21 " --> pdb=" O LYS P 35 " (cutoff:3.500A) removed outlier: 5.426A 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: 15.382A pdb=" N VAL Q 5 " --> pdb=" O GLN Q 26 " (cutoff:3.500A) removed outlier: 11.625A pdb=" N GLN Q 26 " --> pdb=" O VAL Q 5 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR Q 7 " --> pdb=" O GLU Q 24 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU Q 24 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR Q 20 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Q' and resid 55 through 58 removed outlier: 5.845A pdb=" N GLU Q 58 " --> pdb=" O LEU Q 76 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU Q 76 " --> pdb=" O GLU Q 58 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 31 through 33 Processing sheet with id= T, first strand: chain 'X' and resid 28 through 30 removed outlier: 3.603A pdb=" N MET X 29 " --> pdb=" O VAL X 16 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL X 19 " --> pdb=" O PRO X 55 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA X 57 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY X 49 " --> pdb=" O VAL X 56 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG X 58 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU X 47 " --> pdb=" O ARG X 58 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 85 through 91 removed outlier: 6.079A pdb=" N LYS X 115 " --> pdb=" O LYS X 86 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE X 88 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS X 117 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE X 90 " --> pdb=" O LYS X 117 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR X 119 " --> pdb=" O PHE X 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET X 152 " --> pdb=" O LEU X 164 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA X 166 " --> pdb=" O VAL X 150 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL X 150 " --> pdb=" O ALA X 166 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1395 hydrogen bonds 2398 hydrogen bond angles 0 basepair planarities 520 basepair parallelities 881 stacking parallelities Total time for adding SS restraints: 43.35 Time building geometry restraints manager: 25.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6384 1.32 - 1.45: 25137 1.45 - 1.57: 24722 1.57 - 1.70: 3215 1.70 - 1.82: 103 Bond restraints: 59561 Sorted by residual: bond pdb=" C4 5MU Z 54 " pdb=" C5 5MU Z 54 " ideal model delta sigma weight residual 1.802 1.490 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" N1 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.635 1.360 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C5 5MU Z 54 " pdb=" C6 5MU Z 54 " ideal model delta sigma weight residual 1.155 1.404 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" N3 5MU Z 54 " pdb=" C4 5MU Z 54 " ideal model delta sigma weight residual 1.182 1.341 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C2 4SU Z 8 " pdb=" N3 4SU Z 8 " ideal model delta sigma weight residual 1.498 1.350 0.148 2.00e-02 2.50e+03 5.44e+01 ... (remaining 59556 not shown) Histogram of bond angle deviations from ideal: 83.86 - 94.55: 1 94.55 - 105.24: 7498 105.24 - 115.94: 42789 115.94 - 126.63: 33438 126.63 - 137.32: 4647 Bond angle restraints: 88373 Sorted by residual: angle pdb=" N GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta sigma weight residual 110.95 83.86 27.09 1.73e+00 3.34e-01 2.45e+02 angle pdb=" O3' G A 266 " pdb=" C3' G A 266 " pdb=" C2' G A 266 " ideal model delta sigma weight residual 109.50 126.87 -17.37 1.50e+00 4.44e-01 1.34e+02 angle pdb=" O3' C A1145 " pdb=" C3' C A1145 " pdb=" C2' C A1145 " ideal model delta sigma weight residual 109.50 125.58 -16.08 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' U A1498 " pdb=" C3' U A1498 " pdb=" C2' U A1498 " ideal model delta sigma weight residual 109.50 124.96 -15.46 1.50e+00 4.44e-01 1.06e+02 angle pdb=" C GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta sigma weight residual 111.23 96.78 14.45 1.42e+00 4.96e-01 1.04e+02 ... (remaining 88368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 32004 35.83 - 71.66: 4837 71.66 - 107.48: 635 107.48 - 143.31: 22 143.31 - 179.14: 52 Dihedral angle restraints: 37550 sinusoidal: 30232 harmonic: 7318 Sorted by residual: dihedral pdb=" N GLU X 4 " pdb=" C GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta harmonic sigma weight residual 122.80 87.21 35.59 0 2.50e+00 1.60e-01 2.03e+02 dihedral pdb=" C GLU X 4 " pdb=" N GLU X 4 " pdb=" CA GLU X 4 " pdb=" CB GLU X 4 " ideal model delta harmonic sigma weight residual -122.60 -94.01 -28.59 0 2.50e+00 1.60e-01 1.31e+02 dihedral pdb=" C5' U A 560 " pdb=" C4' U A 560 " pdb=" C3' U A 560 " pdb=" O3' U A 560 " ideal model delta sinusoidal sigma weight residual 147.00 66.87 80.13 1 8.00e+00 1.56e-02 1.24e+02 ... (remaining 37547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 10144 0.214 - 0.427: 887 0.427 - 0.641: 30 0.641 - 0.854: 19 0.854 - 1.068: 3 Chirality restraints: 11083 Sorted by residual: 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 -1.68 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C3' A A 792 " pdb=" C4' A A 792 " pdb=" O3' A A 792 " pdb=" C2' A A 792 " both_signs ideal model delta sigma weight residual False -2.74 -1.81 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" C3' U A1498 " pdb=" C4' U A1498 " pdb=" O3' U A1498 " pdb=" C2' U A1498 " both_signs ideal model delta sigma weight residual False -2.74 -1.83 -0.91 2.00e-01 2.50e+01 2.07e+01 ... (remaining 11080 not shown) Planarity restraints: 5227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M Z 46 " -0.112 2.00e-02 2.50e+03 4.46e-01 4.47e+03 pdb=" C4' G7M Z 46 " -0.382 2.00e-02 2.50e+03 pdb=" O4' G7M Z 46 " -0.238 2.00e-02 2.50e+03 pdb=" C3' G7M Z 46 " 0.551 2.00e-02 2.50e+03 pdb=" O3' G7M Z 46 " 0.447 2.00e-02 2.50e+03 pdb=" C2' G7M Z 46 " 0.233 2.00e-02 2.50e+03 pdb=" O2' G7M Z 46 " -0.808 2.00e-02 2.50e+03 pdb=" C1' G7M Z 46 " -0.242 2.00e-02 2.50e+03 pdb=" N9 G7M Z 46 " 0.550 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 4SU Z 8 " -0.284 2.00e-02 2.50e+03 4.43e-01 4.42e+03 pdb=" C4' 4SU Z 8 " 0.402 2.00e-02 2.50e+03 pdb=" O4' 4SU Z 8 " 0.738 2.00e-02 2.50e+03 pdb=" C3' 4SU Z 8 " -0.486 2.00e-02 2.50e+03 pdb=" O3' 4SU Z 8 " -0.090 2.00e-02 2.50e+03 pdb=" C2' 4SU Z 8 " -0.377 2.00e-02 2.50e+03 pdb=" O2' 4SU Z 8 " 0.410 2.00e-02 2.50e+03 pdb=" C1' 4SU Z 8 " 0.279 2.00e-02 2.50e+03 pdb=" N1 4SU Z 8 " -0.593 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC Z 32 " -0.033 2.00e-02 2.50e+03 4.36e-01 4.27e+03 pdb=" C4' OMC Z 32 " 0.401 2.00e-02 2.50e+03 pdb=" O4' OMC Z 32 " 0.407 2.00e-02 2.50e+03 pdb=" C3' OMC Z 32 " -0.561 2.00e-02 2.50e+03 pdb=" O3' OMC Z 32 " -0.305 2.00e-02 2.50e+03 pdb=" C2' OMC Z 32 " -0.298 2.00e-02 2.50e+03 pdb=" O2' OMC Z 32 " 0.702 2.00e-02 2.50e+03 pdb=" C1' OMC Z 32 " 0.259 2.00e-02 2.50e+03 pdb=" N1 OMC Z 32 " -0.571 2.00e-02 2.50e+03 ... (remaining 5224 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 39 2.01 - 2.73: 5769 2.73 - 3.46: 81072 3.46 - 4.18: 188088 4.18 - 4.90: 247672 Nonbonded interactions: 522640 Sorted by model distance: nonbonded pdb=" O LYS X 3 " pdb=" NH1 ARG X 66 " model vdw 1.289 2.520 nonbonded pdb=" OP1 C A 578 " pdb="MG MG A1668 " model vdw 1.364 2.170 nonbonded pdb=" OP2 G A 597 " pdb="MG MG A1634 " model vdw 1.368 2.170 nonbonded pdb=" OP2 A A 195 " pdb="MG MG A1609 " model vdw 1.370 2.170 nonbonded pdb=" OP2 C A 352 " pdb="MG MG A1639 " model vdw 1.416 2.170 ... (remaining 522635 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: 0.730 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: 0.040 Extract box with map and model: 5.890 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 159.730 Find NCS groups from input model: 0.890 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.312 59561 Z= 0.502 Angle : 1.439 27.088 88373 Z= 0.958 Chirality : 0.121 1.068 11083 Planarity : 0.016 0.446 5227 Dihedral : 26.674 179.138 32846 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 3.75 % Allowed : 12.01 % Favored : 84.24 % Rotamer: Outliers : 25.30 % Allowed : 19.49 % Favored : 55.20 % Cbeta Deviations : 1.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2506 helix: 0.15 (0.14), residues: 986 sheet: -1.89 (0.25), residues: 367 loop : -3.44 (0.14), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP P 59 HIS 0.010 0.002 HIS G 153 PHE 0.019 0.003 PHE R 81 TYR 0.031 0.003 TYR L 120 ARG 0.026 0.002 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 540 poor density : 1047 time to evaluate : 2.634 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 outliers start: 540 outliers final: 108 residues processed: 1309 average time/residue: 0.6665 time to fit residues: 1346.0420 Evaluate side-chains 773 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 665 time to evaluate : 2.547 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 108 outliers final: 1 residues processed: 108 average time/residue: 0.4888 time to fit residues: 94.1956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 0.5980 chunk 316 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN B 37 ASN B 140 HIS B 146 GLN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 HIS D 42 GLN D 77 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN E 72 GLN E 73 ASN F 7 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 HIS ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 HIS J 56 HIS ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** L 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS M 62 ASN O 37 ASN P 13 HIS ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 59561 Z= 0.308 Angle : 0.883 14.690 88373 Z= 0.458 Chirality : 0.044 0.344 11083 Planarity : 0.007 0.120 5227 Dihedral : 25.227 179.965 27514 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.66 % Favored : 90.50 % Rotamer: Outliers : 6.42 % Allowed : 28.91 % Favored : 64.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.55 (0.16), residues: 2506 helix: 1.12 (0.17), residues: 985 sheet: -1.35 (0.25), residues: 366 loop : -2.99 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 138 HIS 0.020 0.002 HIS H 82 PHE 0.021 0.003 PHE X 90 TYR 0.026 0.002 TYR O 78 ARG 0.014 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 773 time to evaluate : 2.584 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 outliers start: 137 outliers final: 60 residues processed: 846 average time/residue: 0.5714 time to fit residues: 792.6801 Evaluate side-chains 699 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 639 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4265 time to fit residues: 50.1784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 305 optimal weight: 0.1980 chunk 249 optimal weight: 7.9990 chunk 101 optimal weight: 30.0000 chunk 367 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 364 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN B 224 GLN D 77 ASN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 7 ASN F 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN X 15 GLN ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 59561 Z= 0.323 Angle : 0.817 14.842 88373 Z= 0.423 Chirality : 0.042 0.314 11083 Planarity : 0.007 0.118 5227 Dihedral : 24.883 179.850 27514 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 26.90 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.18 % Favored : 90.14 % Rotamer: Outliers : 5.44 % Allowed : 29.85 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.61 (0.16), residues: 2506 helix: 0.76 (0.16), residues: 970 sheet: -1.22 (0.24), residues: 378 loop : -2.72 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP X 65 HIS 0.016 0.002 HIS H 82 PHE 0.029 0.003 PHE B 55 TYR 0.023 0.002 TYR I 88 ARG 0.008 0.001 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 679 time to evaluate : 2.870 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 outliers start: 116 outliers final: 62 residues processed: 752 average time/residue: 0.5740 time to fit residues: 713.0312 Evaluate side-chains 672 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 610 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.4549 time to fit residues: 53.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 368 optimal weight: 10.0000 chunk 390 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 82 HIS ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 59561 Z= 0.323 Angle : 0.788 13.287 88373 Z= 0.410 Chirality : 0.041 0.309 11083 Planarity : 0.007 0.117 5227 Dihedral : 24.745 179.819 27514 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.38 % Favored : 90.98 % Rotamer: Outliers : 5.30 % Allowed : 31.02 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.62 (0.16), residues: 2506 helix: 0.54 (0.16), residues: 991 sheet: -1.23 (0.25), residues: 366 loop : -2.56 (0.16), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP G 103 HIS 0.016 0.002 HIS H 82 PHE 0.027 0.003 PHE B 55 TYR 0.019 0.002 TYR N 21 ARG 0.017 0.001 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 654 time to evaluate : 2.599 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 outliers start: 113 outliers final: 55 residues processed: 716 average time/residue: 0.5758 time to fit residues: 677.2331 Evaluate side-chains 626 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 571 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4226 time to fit residues: 46.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 290 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 333 optimal weight: 0.9990 chunk 269 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 100 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN X 129 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 59561 Z= 0.341 Angle : 0.800 13.424 88373 Z= 0.414 Chirality : 0.041 0.313 11083 Planarity : 0.007 0.117 5227 Dihedral : 24.715 179.277 27514 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 28.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.82 % Favored : 90.54 % Rotamer: Outliers : 3.66 % Allowed : 32.90 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.92 % 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: -1.74 (0.16), residues: 2506 helix: 0.33 (0.16), residues: 989 sheet: -1.31 (0.24), residues: 371 loop : -2.50 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 103 HIS 0.013 0.002 HIS K 116 PHE 0.022 0.003 PHE Q 71 TYR 0.034 0.002 TYR O 78 ARG 0.016 0.001 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 620 time to evaluate : 2.643 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 outliers start: 78 outliers final: 44 residues processed: 667 average time/residue: 0.5856 time to fit residues: 644.5528 Evaluate side-chains 623 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 579 time to evaluate : 2.586 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.4226 time to fit residues: 37.6614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 10.0000 chunk 351 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 390 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 73 ASN F 100 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN O 62 GLN ** S 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 59561 Z= 0.212 Angle : 0.714 13.429 88373 Z= 0.372 Chirality : 0.036 0.301 11083 Planarity : 0.006 0.115 5227 Dihedral : 24.555 179.931 27514 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.10 % Favored : 92.30 % Rotamer: Outliers : 2.81 % Allowed : 34.30 % Favored : 62.89 % 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: -1.44 (0.16), residues: 2506 helix: 0.56 (0.16), residues: 972 sheet: -1.05 (0.25), residues: 366 loop : -2.31 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 97 HIS 0.010 0.001 HIS K 116 PHE 0.029 0.002 PHE B 55 TYR 0.025 0.002 TYR F 4 ARG 0.008 0.001 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 647 time to evaluate : 2.639 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 outliers start: 60 outliers final: 32 residues processed: 672 average time/residue: 0.5728 time to fit residues: 638.2198 Evaluate side-chains 618 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 586 time to evaluate : 2.576 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4272 time to fit residues: 28.2038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 0.0370 chunk 44 optimal weight: 20.0000 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 329 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 389 optimal weight: 0.3980 chunk 243 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 179 optimal weight: 20.0000 overall best weight: 3.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN F 100 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN R 36 ASN S 47 HIS T 42 GLN T 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 59561 Z= 0.224 Angle : 0.719 14.363 88373 Z= 0.373 Chirality : 0.037 0.393 11083 Planarity : 0.006 0.116 5227 Dihedral : 24.507 179.376 27514 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.66 % Favored : 91.74 % Rotamer: Outliers : 2.81 % Allowed : 35.38 % Favored : 61.81 % 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 (0.16), residues: 2506 helix: 0.49 (0.16), residues: 970 sheet: -0.96 (0.25), residues: 365 loop : -2.23 (0.17), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 103 HIS 0.009 0.001 HIS K 116 PHE 0.032 0.002 PHE G 26 TYR 0.018 0.002 TYR F 4 ARG 0.011 0.001 ARG Q 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 626 time to evaluate : 2.589 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 outliers start: 60 outliers final: 26 residues processed: 653 average time/residue: 0.5664 time to fit residues: 616.8658 Evaluate side-chains 611 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 585 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4646 time to fit residues: 24.6168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 232 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS ** B 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 37 GLN ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS T 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 59561 Z= 0.348 Angle : 0.800 13.449 88373 Z= 0.412 Chirality : 0.040 0.300 11083 Planarity : 0.007 0.117 5227 Dihedral : 24.567 178.015 27514 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 28.83 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.54 % Favored : 90.90 % Rotamer: Outliers : 2.48 % Allowed : 36.64 % Favored : 60.87 % 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: -1.67 (0.16), residues: 2506 helix: 0.15 (0.16), residues: 974 sheet: -1.13 (0.25), residues: 370 loop : -2.24 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 97 HIS 0.008 0.002 HIS K 116 PHE 0.037 0.003 PHE B 55 TYR 0.020 0.002 TYR F 4 ARG 0.015 0.001 ARG Q 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 599 time to evaluate : 2.625 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 outliers start: 53 outliers final: 38 residues processed: 617 average time/residue: 0.5837 time to fit residues: 598.8498 Evaluate side-chains 608 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 570 time to evaluate : 2.584 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4132 time to fit residues: 32.5605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 362 optimal weight: 10.0000 chunk 372 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 284 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 327 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN F 100 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN J 78 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN T 42 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 59561 Z= 0.234 Angle : 0.736 15.037 88373 Z= 0.381 Chirality : 0.037 0.286 11083 Planarity : 0.006 0.116 5227 Dihedral : 24.490 178.196 27514 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.78 % Favored : 91.62 % Rotamer: Outliers : 0.89 % Allowed : 38.05 % Favored : 61.06 % 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: -1.57 (0.16), residues: 2506 helix: 0.22 (0.16), residues: 975 sheet: -1.08 (0.25), residues: 368 loop : -2.17 (0.17), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 97 HIS 0.007 0.001 HIS K 116 PHE 0.024 0.002 PHE G 26 TYR 0.016 0.002 TYR P 38 ARG 0.009 0.001 ARG Q 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 608 time to evaluate : 2.641 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 outliers start: 19 outliers final: 13 residues processed: 616 average time/residue: 0.5781 time to fit residues: 593.0677 Evaluate side-chains 584 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 571 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4450 time to fit residues: 13.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 383 optimal weight: 0.9990 chunk 234 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 402 optimal weight: 20.0000 chunk 370 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 59561 Z= 0.230 Angle : 0.732 13.535 88373 Z= 0.379 Chirality : 0.036 0.279 11083 Planarity : 0.006 0.116 5227 Dihedral : 24.450 177.627 27514 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.82 % Favored : 91.58 % Rotamer: Outliers : 0.66 % Allowed : 38.66 % Favored : 60.68 % 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: -1.56 (0.16), residues: 2506 helix: 0.18 (0.16), residues: 980 sheet: -1.01 (0.25), residues: 364 loop : -2.13 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 97 HIS 0.006 0.001 HIS K 116 PHE 0.032 0.003 PHE B 55 TYR 0.022 0.002 TYR H 48 ARG 0.011 0.001 ARG Q 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 590 time to evaluate : 2.579 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 outliers start: 14 outliers final: 5 residues processed: 595 average time/residue: 0.5656 time to fit residues: 563.2926 Evaluate side-chains 562 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 557 time to evaluate : 2.581 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3871 time to fit residues: 6.6820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 0.8980 chunk 254 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 295 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN T 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.081681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067575 restraints weight = 210313.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069255 restraints weight = 81059.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.070224 restraints weight = 46142.365| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 59561 Z= 0.318 Angle : 0.788 15.040 88373 Z= 0.406 Chirality : 0.039 0.321 11083 Planarity : 0.007 0.117 5227 Dihedral : 24.490 177.375 27514 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 27.69 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.62 % Favored : 90.78 % Rotamer: Outliers : 1.08 % Allowed : 38.57 % Favored : 60.36 % 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: -1.71 (0.16), residues: 2506 helix: -0.00 (0.16), residues: 979 sheet: -1.05 (0.25), residues: 362 loop : -2.18 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 97 HIS 0.006 0.001 HIS K 116 PHE 0.029 0.003 PHE B 28 TYR 0.024 0.002 TYR H 48 ARG 0.014 0.001 ARG Q 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11144.35 seconds wall clock time: 198 minutes 35.00 seconds (11915.00 seconds total)