Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 16:56:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_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_4080/04_2023/5lmu_4080_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lmu_4080/04_2023/5lmu_4080_neut_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 21.78, per 1000 atoms: 0.39 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: 27.98 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 300 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 9 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 26 " pdb="ZN ZN D 300 " - pdb=" SG CYS D 31 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 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: 21.78 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: 42.21 Time building geometry restraints manager: 29.69 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: 29676 35.83 - 71.66: 2350 71.66 - 107.48: 184 107.48 - 143.31: 22 143.31 - 179.14: 50 Dihedral angle restraints: 32282 sinusoidal: 24964 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 32279 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: 0.680 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: 7.740 Check model and map are aligned: 0.660 Set scattering table: 0.370 Process input model: 162.540 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.580 ------------------------------------------------------------------------------- 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 : 21.344 179.138 27578 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 % 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 *********************** 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 : 2.848 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: 0.6803 time to fit residues: 1382.4920 Evaluate side-chains 773 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 665 time to evaluate : 2.873 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 108 outliers final: 1 residues processed: 108 average time/residue: 0.5270 time to fit residues: 102.8017 ------------------------------------------------------------------------------- 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 37 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 59561 Z= 0.294 Angle : 0.878 14.341 88373 Z= 0.455 Chirality : 0.044 0.341 11083 Planarity : 0.007 0.124 5227 Dihedral : 17.475 179.711 22246 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.30 % Favored : 90.86 % Rotamer Outliers : 6.70 % 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: 1.13 (0.17), residues: 980 sheet: -1.34 (0.25), residues: 366 loop : -2.98 (0.15), residues: 1160 *********************** 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 916 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 773 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 outliers start: 143 outliers final: 58 residues processed: 850 average time/residue: 0.5821 time to fit residues: 817.4458 Evaluate side-chains 691 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 633 time to evaluate : 2.843 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4060 time to fit residues: 48.1180 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 20.0000 chunk 305 optimal weight: 0.4980 chunk 249 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 367 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 chunk 364 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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 76 GLN 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 72 GLN E 73 ASN F 32 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 GLN G 110 GLN ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS Q 45 HIS ** R 36 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.081 59561 Z= 0.307 Angle : 0.795 13.366 88373 Z= 0.414 Chirality : 0.041 0.319 11083 Planarity : 0.007 0.119 5227 Dihedral : 16.915 179.889 22246 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.02 % Favored : 90.30 % Rotamer Outliers : 5.48 % 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: -1.54 (0.16), residues: 2506 helix: 0.83 (0.16), residues: 970 sheet: -1.28 (0.24), residues: 391 loop : -2.67 (0.16), residues: 1145 *********************** 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: 117 poor density : 678 time to evaluate : 2.884 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: 117 outliers final: 65 residues processed: 748 average time/residue: 0.5801 time to fit residues: 717.5234 Evaluate side-chains 671 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 606 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.4579 time to fit residues: 57.4347 ------------------------------------------------------------------------------- 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: 20.0000 chunk 190 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 246 optimal weight: 0.6980 chunk 368 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 349 optimal weight: 0.3980 chunk 105 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 26 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 47 HIS ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 59561 Z= 0.246 Angle : 0.734 13.223 88373 Z= 0.384 Chirality : 0.038 0.312 11083 Planarity : 0.006 0.116 5227 Dihedral : 16.555 177.952 22246 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.50 % Favored : 91.90 % Rotamer Outliers : 4.17 % 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: -1.38 (0.16), residues: 2506 helix: 0.82 (0.16), residues: 974 sheet: -1.12 (0.25), residues: 362 loop : -2.45 (0.16), residues: 1170 *********************** 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 759 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 670 time to evaluate : 2.887 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: 89 outliers final: 39 residues processed: 721 average time/residue: 0.5740 time to fit residues: 688.9537 Evaluate side-chains 644 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 605 time to evaluate : 2.851 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4479 time to fit residues: 34.9926 ------------------------------------------------------------------------------- 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: 4.9990 chunk 221 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 chunk 161 optimal weight: 30.0000 chunk 333 optimal weight: 0.9980 chunk 269 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 350 optimal weight: 0.0870 chunk 98 optimal weight: 20.0000 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 F 100 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 59561 Z= 0.180 Angle : 0.704 16.456 88373 Z= 0.367 Chirality : 0.036 0.306 11083 Planarity : 0.006 0.115 5227 Dihedral : 16.312 178.948 22246 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.02 % Favored : 92.34 % Rotamer Outliers : 3.00 % 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: -1.22 (0.16), residues: 2506 helix: 0.84 (0.17), residues: 969 sheet: -1.02 (0.25), residues: 376 loop : -2.25 (0.17), residues: 1161 *********************** 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 727 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 663 time to evaluate : 3.026 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: 64 outliers final: 31 residues processed: 692 average time/residue: 0.5903 time to fit residues: 674.6658 Evaluate side-chains 629 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 598 time to evaluate : 2.868 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.4262 time to fit residues: 28.6238 ------------------------------------------------------------------------------- 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: 0.0980 chunk 77 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 324 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 overall best weight: 7.6192 ------------------------------------------------------------------------------- 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 94 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN E 38 GLN E 73 ASN F 27 GLN F 100 ASN G 56 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 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: 0.7795 moved from start: 0.5288 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= 0.381 Angle : 0.828 14.950 88373 Z= 0.427 Chirality : 0.042 0.311 11083 Planarity : 0.007 0.117 5227 Dihedral : 16.637 178.933 22246 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 30.26 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.54 % Favored : 90.86 % Rotamer Outliers : 3.66 % 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: -1.59 (0.16), residues: 2506 helix: 0.34 (0.16), residues: 988 sheet: -1.13 (0.24), residues: 375 loop : -2.32 (0.17), residues: 1143 *********************** 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 694 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 616 time to evaluate : 3.023 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: 78 outliers final: 47 residues processed: 650 average time/residue: 0.5843 time to fit residues: 631.6215 Evaluate side-chains 635 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 588 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.4242 time to fit residues: 40.6363 ------------------------------------------------------------------------------- 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: 9.9990 chunk 44 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 329 optimal weight: 9.9990 chunk 218 optimal weight: 4.9990 chunk 389 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 HIS B 94 ASN B 146 GLN C 162 GLN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 199 ASN ** 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** L 8 ASN O 62 GLN Q 26 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.004 0.084 59561 Z= 0.276 Angle : 0.756 19.871 88373 Z= 0.392 Chirality : 0.039 0.359 11083 Planarity : 0.006 0.116 5227 Dihedral : 16.451 179.820 22246 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.50 % Favored : 91.94 % Rotamer Outliers : 2.25 % 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: -1.46 (0.16), residues: 2506 helix: 0.48 (0.16), residues: 970 sheet: -1.10 (0.24), residues: 380 loop : -2.24 (0.17), residues: 1156 *********************** 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 684 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 636 time to evaluate : 2.883 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 outliers start: 48 outliers final: 26 residues processed: 658 average time/residue: 0.5807 time to fit residues: 639.3845 Evaluate side-chains 616 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 590 time to evaluate : 2.872 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4135 time to fit residues: 23.6824 ------------------------------------------------------------------------------- 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: 10.0000 chunk 155 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 265 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 306 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 224 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** 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** ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN Q 26 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN T 90 GLN ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 59561 Z= 0.239 Angle : 0.736 18.616 88373 Z= 0.381 Chirality : 0.037 0.297 11083 Planarity : 0.006 0.116 5227 Dihedral : 16.300 178.523 22246 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.78 % Favored : 91.66 % Rotamer Outliers : 1.83 % 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: -1.46 (0.16), residues: 2506 helix: 0.42 (0.16), residues: 965 sheet: -1.10 (0.25), residues: 357 loop : -2.14 (0.17), residues: 1184 *********************** 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 665 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 626 time to evaluate : 2.859 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: 39 outliers final: 24 residues processed: 644 average time/residue: 0.5638 time to fit residues: 609.1343 Evaluate side-chains 620 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 596 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4240 time to fit residues: 22.3533 ------------------------------------------------------------------------------- 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: 2.9990 chunk 373 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 362 optimal weight: 0.4980 chunk 372 optimal weight: 5.9990 chunk 218 optimal weight: 6.9990 chunk 158 optimal weight: 40.0000 chunk 284 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 327 optimal weight: 0.9990 chunk 343 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** 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 119 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN ** X 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 59561 Z= 0.173 Angle : 0.699 22.262 88373 Z= 0.361 Chirality : 0.035 0.273 11083 Planarity : 0.006 0.115 5227 Dihedral : 15.986 179.998 22246 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 20.94 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.38 % Favored : 93.14 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 2506 helix: 0.57 (0.17), residues: 951 sheet: -0.97 (0.25), residues: 360 loop : -1.99 (0.17), residues: 1195 *********************** 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 667 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 647 time to evaluate : 2.859 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 outliers start: 20 outliers final: 11 residues processed: 659 average time/residue: 0.5971 time to fit residues: 651.0497 Evaluate side-chains 599 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 588 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4470 time to fit residues: 12.5407 ------------------------------------------------------------------------------- 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: 7.9990 chunk 238 optimal weight: 9.9990 chunk 383 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 266 optimal weight: 0.0470 chunk 402 optimal weight: 30.0000 chunk 370 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** 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 119 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN Q 26 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN X 129 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6038 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= 0.273 Angle : 0.761 15.922 88373 Z= 0.391 Chirality : 0.037 0.279 11083 Planarity : 0.006 0.116 5227 Dihedral : 16.109 177.446 22246 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 26.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.66 % Favored : 91.82 % Rotamer Outliers : 0.80 % 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: -1.47 (0.16), residues: 2506 helix: 0.26 (0.16), residues: 975 sheet: -1.03 (0.25), residues: 357 loop : -2.06 (0.17), residues: 1174 ********************** 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 615 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 598 time to evaluate : 2.995 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 outliers start: 17 outliers final: 12 residues processed: 604 average time/residue: 0.5821 time to fit residues: 587.0117 Evaluate side-chains 590 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 578 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4529 time to fit residues: 13.3882 ------------------------------------------------------------------------------- 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: 10.0000 chunk 254 optimal weight: 5.9990 chunk 341 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 119 GLN ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070108 restraints weight = 211226.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.072033 restraints weight = 90513.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.072384 restraints weight = 45950.583| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 59561 Z= 0.276 Angle : 0.763 15.825 88373 Z= 0.394 Chirality : 0.038 0.283 11083 Planarity : 0.006 0.116 5227 Dihedral : 16.158 177.923 22246 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.74 % Favored : 91.74 % Rotamer Outliers : 0.75 % 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: 0.17 (0.16), residues: 966 sheet: -1.07 (0.25), residues: 358 loop : -2.09 (0.17), residues: 1182 =============================================================================== Job complete usr+sys time: 10926.98 seconds wall clock time: 194 minutes 43.61 seconds (11683.61 seconds total)