Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:47:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/02_2023/7zyv_15027_trim_updated.pdb" } resolution = 2.13 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= 0.001 sd= 0.042 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 Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 64": "OD1" <-> "OD2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ASP 87": "OD1" <-> "OD2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K ASP 224": "OD1" <-> "OD2" Residue "K ASP 240": "OD1" <-> "OD2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L ARG 137": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R ASP 52": "OD1" <-> "OD2" Residue "Q PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16452 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1225 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2158 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 23, 'TRANS': 254} Chain breaks: 1 Chain: "D" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1259 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2167 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1254 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain breaks: 1 Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 317 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'UMQ': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'HEC': 1, 'PL9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'BCR': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5784 SG CYS D 107 42.317 69.391 44.000 1.00 96.15 S ATOM 5920 SG CYS D 125 40.722 65.931 43.166 1.00 95.70 S ATOM 13133 SG CYS L 107 93.565 26.930 43.993 1.00 96.40 S ATOM 13269 SG CYS L 125 95.166 30.393 43.162 1.00 96.16 S Time building chain proxies: 9.90, per 1000 atoms: 0.60 Number of scatterers: 16452 At special positions: 0 Unit cell: (136.74, 97.18, 122.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 2858 8.00 N 2500 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " distance=2.03 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 125 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 109 " pdb=" FES L 402 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 11 sheets defined 47.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.811A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.537A pdb=" N SER A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 56 removed outlier: 4.546A pdb=" N GLY A 37 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.671A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 4.388A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.857A pdb=" N GLY A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 190 through 209 Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.641A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 79 through 88 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 94 through 114 removed outlier: 4.031A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.753A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 127 through 148 removed outlier: 4.498A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 20 through 23 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 248 through 282 removed outlier: 3.654A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 41 removed outlier: 3.650A pdb=" N SER D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix removed outlier: 4.134A pdb=" N PHE D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 removed outlier: 3.985A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.836A pdb=" N THR F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 31 removed outlier: 3.876A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 3 through 25 removed outlier: 3.752A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 12 removed outlier: 3.811A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.537A pdb=" N SER I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 removed outlier: 4.546A pdb=" N GLY I 37 " --> pdb=" O TYR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 Processing helix chain 'I' and resid 79 through 106 removed outlier: 3.671A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 137 removed outlier: 4.388A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 157 removed outlier: 3.856A pdb=" N GLY I 153 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL I 154 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Proline residue: I 155 - end of helix Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'I' and resid 190 through 209 Processing helix chain 'J' and resid 12 through 20 removed outlier: 3.642A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 57 Processing helix chain 'J' and resid 79 through 88 Proline residue: J 83 - end of helix Processing helix chain 'J' and resid 94 through 114 removed outlier: 4.031A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.753A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL J 111 " --> pdb=" O GLY J 107 " (cutoff:3.500A) Proline residue: J 112 - end of helix Processing helix chain 'J' and resid 123 through 125 No H-bonds generated for 'chain 'J' and resid 123 through 125' Processing helix chain 'J' and resid 127 through 148 removed outlier: 4.498A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 20 through 23 Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 91 through 97 Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 248 through 282 removed outlier: 3.654A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 41 removed outlier: 3.556A pdb=" N GLU L 16 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix removed outlier: 3.678A pdb=" N LEU L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Proline residue: L 36 - end of helix removed outlier: 4.133A pdb=" N PHE L 41 " --> pdb=" O TYR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 71 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 27 Processing helix chain 'N' and resid 2 through 35 removed outlier: 3.872A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 31 removed outlier: 3.876A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 25 Processing helix chain 'R' and resid 36 through 42 removed outlier: 3.550A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 42 removed outlier: 3.550A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'C' and resid 38 through 40 removed outlier: 8.493A pdb=" N VAL C 39 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 244 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 204 through 207 removed outlier: 7.016A pdb=" N ALA C 195 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 179 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.592A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= F, first strand: chain 'D' and resid 115 through 117 Processing sheet with id= G, first strand: chain 'K' and resid 32 through 34 Processing sheet with id= H, first strand: chain 'K' and resid 38 through 40 removed outlier: 8.494A pdb=" N VAL K 39 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL K 244 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 203 through 207 removed outlier: 7.017A pdb=" N ALA K 195 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL K 179 " --> pdb=" O ALA K 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.576A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 101 through 103 701 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 7.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 6621 1.41 - 1.61: 10127 1.61 - 1.81: 110 1.81 - 2.01: 4 2.01 - 2.20: 48 Bond restraints: 16910 Sorted by residual: bond pdb=" C1 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 SQD D 201 " pdb=" O5 SQD D 201 " ideal model delta sigma weight residual 1.500 1.398 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5' UMQ B 403 " pdb=" O5' UMQ B 403 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C5' UMQ J 404 " pdb=" O5' UMQ J 404 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C5 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.483 1.402 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 16905 not shown) Histogram of bond angle deviations from ideal: 75.57 - 96.38: 44 96.38 - 117.20: 12322 117.20 - 138.02: 10711 138.02 - 158.84: 2 158.84 - 179.65: 20 Bond angle restraints: 23099 Sorted by residual: angle pdb=" N ARG E 29 " pdb=" CA ARG E 29 " pdb=" C ARG E 29 " ideal model delta sigma weight residual 112.86 117.39 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CG LYS C 222 " pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " ideal model delta sigma weight residual 111.30 119.56 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CG LYS K 222 " pdb=" CD LYS K 222 " pdb=" CE LYS K 222 " ideal model delta sigma weight residual 111.30 119.55 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N LYS B 119 " pdb=" CA LYS B 119 " pdb=" C LYS B 119 " ideal model delta sigma weight residual 112.59 116.63 -4.04 1.22e+00 6.72e-01 1.10e+01 angle pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " pdb=" NZ LYS C 222 " ideal model delta sigma weight residual 111.90 122.45 -10.55 3.20e+00 9.77e-02 1.09e+01 ... (remaining 23094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 8684 24.26 - 48.51: 764 48.51 - 72.77: 163 72.77 - 97.02: 30 97.02 - 121.28: 2 Dihedral angle restraints: 9643 sinusoidal: 4095 harmonic: 5548 Sorted by residual: dihedral pdb=" CA LYS D 96 " pdb=" C LYS D 96 " pdb=" N THR D 97 " pdb=" CA THR D 97 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C1 BCR P 101 " pdb=" C2 BCR P 101 " pdb=" C3 BCR P 101 " pdb=" C4 BCR P 101 " ideal model delta sinusoidal sigma weight residual -60.86 60.42 -121.28 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CA LYS K 222 " pdb=" C LYS K 222 " pdb=" N LEU K 223 " pdb=" CA LEU K 223 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 9640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2531 0.121 - 0.243: 34 0.243 - 0.364: 4 0.364 - 0.486: 1 0.486 - 0.607: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" C1 UMQ B 403 " pdb=" C2 UMQ B 403 " pdb=" O1 UMQ B 403 " pdb=" O5 UMQ B 403 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" C1 UMQ J 404 " pdb=" C2 UMQ J 404 " pdb=" O1 UMQ J 404 " pdb=" O5 UMQ J 404 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" C1 SQD D 201 " pdb=" C2 SQD D 201 " pdb=" O5 SQD D 201 " pdb=" O6 SQD D 201 " both_signs ideal model delta sigma weight residual False -2.39 -2.02 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2569 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 SQD L 401 " 0.101 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C8 SQD L 401 " -0.030 2.00e-02 2.50e+03 pdb=" O47 SQD L 401 " -0.033 2.00e-02 2.50e+03 pdb=" O49 SQD L 401 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR F 101 " 0.038 2.00e-02 2.50e+03 3.89e-02 1.89e+01 pdb=" C21 BCR F 101 " -0.066 2.00e-02 2.50e+03 pdb=" C22 BCR F 101 " 0.033 2.00e-02 2.50e+03 pdb=" C23 BCR F 101 " 0.015 2.00e-02 2.50e+03 pdb=" C37 BCR F 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.031 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C21 BCR P 101 " -0.060 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " 0.045 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.006 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.022 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 65 2.52 - 3.12: 11721 3.12 - 3.71: 23031 3.71 - 4.31: 33361 4.31 - 4.90: 57230 Nonbonded interactions: 125408 Sorted by model distance: nonbonded pdb=" O2 UMQ J 404 " pdb=" O3' UMQ J 404 " model vdw 1.927 2.440 nonbonded pdb=" O2 UMQ B 403 " pdb=" O3' UMQ B 403 " model vdw 1.928 2.440 nonbonded pdb=" O2 UMQ A 305 " pdb=" O3' UMQ A 305 " model vdw 1.985 2.440 nonbonded pdb=" O GLY K 177 " pdb=" OG SER K 220 " model vdw 2.003 2.440 nonbonded pdb=" O GLY C 177 " pdb=" OG SER C 220 " model vdw 2.004 2.440 ... (remaining 125403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 215 or resid 301 through 306)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'J' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 401 through 404)) } ncs_group { reference = chain 'C' selection = (chain 'K' and (resid 1 through 195 or resid 203 through 285 or resid 301)) } ncs_group { reference = (chain 'D' and (resid 8 through 178 or resid 201 through 202)) selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = chain 'N' } ncs_group { reference = (chain 'G' and resid 1 through 33) selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 1 through 29) selection = (chain 'P' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)))) } ncs_group { reference = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 Mg 2 5.21 5 S 72 5.16 5 C 11008 2.51 5 N 2500 2.21 5 O 2858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.080 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: 0.010 Extract box with map and model: 13.040 Check model and map are aligned: 0.250 Process input model: 44.060 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 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 : 0.007 0.103 16910 Z= 0.418 Angle : 0.701 10.545 23099 Z= 0.326 Chirality : 0.051 0.607 2572 Planarity : 0.005 0.058 2761 Dihedral : 18.573 121.280 6077 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.99 (0.20), residues: 1902 helix: 2.34 (0.17), residues: 946 sheet: 0.11 (0.37), residues: 188 loop : -1.45 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.974 Fit side-chains outliers start: 36 outliers final: 26 residues processed: 215 average time/residue: 1.6131 time to fit residues: 378.1786 Evaluate side-chains 191 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 1 average time/residue: 1.5415 time to fit residues: 4.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 0.0010 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 16910 Z= 0.229 Angle : 0.676 12.123 23099 Z= 0.311 Chirality : 0.046 0.160 2572 Planarity : 0.006 0.047 2761 Dihedral : 14.167 87.161 2578 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.96 (0.19), residues: 1902 helix: 2.23 (0.17), residues: 961 sheet: -0.08 (0.35), residues: 202 loop : -1.37 (0.21), residues: 739 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 34 residues processed: 216 average time/residue: 1.5153 time to fit residues: 357.9517 Evaluate side-chains 207 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 1.803 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 27 residues processed: 7 average time/residue: 0.8081 time to fit residues: 8.9016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 0.0040 chunk 57 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16910 Z= 0.213 Angle : 0.638 11.376 23099 Z= 0.295 Chirality : 0.044 0.160 2572 Planarity : 0.005 0.052 2761 Dihedral : 13.497 89.048 2578 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.04 (0.19), residues: 1902 helix: 2.25 (0.17), residues: 959 sheet: 0.12 (0.34), residues: 206 loop : -1.32 (0.21), residues: 737 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 176 time to evaluate : 1.900 Fit side-chains revert: symmetry clash outliers start: 55 outliers final: 33 residues processed: 219 average time/residue: 1.4931 time to fit residues: 358.4992 Evaluate side-chains 207 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.831 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 6 average time/residue: 0.9216 time to fit residues: 8.7086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 112 optimal weight: 0.2980 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16910 Z= 0.170 Angle : 0.586 9.713 23099 Z= 0.271 Chirality : 0.043 0.151 2572 Planarity : 0.005 0.050 2761 Dihedral : 13.016 89.756 2578 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.21 (0.20), residues: 1902 helix: 2.37 (0.17), residues: 955 sheet: 0.27 (0.34), residues: 206 loop : -1.21 (0.21), residues: 741 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 30 residues processed: 220 average time/residue: 1.5255 time to fit residues: 368.2071 Evaluate side-chains 212 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 3 average time/residue: 0.2068 time to fit residues: 3.4026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.7928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.177 Angle : 0.590 9.885 23099 Z= 0.273 Chirality : 0.043 0.173 2572 Planarity : 0.005 0.050 2761 Dihedral : 12.895 89.561 2578 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.24 (0.20), residues: 1902 helix: 2.37 (0.17), residues: 955 sheet: 0.33 (0.34), residues: 206 loop : -1.18 (0.21), residues: 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 1.752 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 31 residues processed: 214 average time/residue: 1.5392 time to fit residues: 360.8699 Evaluate side-chains 212 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 1.0117 time to fit residues: 7.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.0980 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 16910 Z= 0.173 Angle : 0.589 9.916 23099 Z= 0.273 Chirality : 0.043 0.201 2572 Planarity : 0.005 0.051 2761 Dihedral : 12.741 89.716 2578 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.29 (0.20), residues: 1902 helix: 2.39 (0.17), residues: 955 sheet: 0.41 (0.34), residues: 206 loop : -1.14 (0.21), residues: 741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.862 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 212 average time/residue: 1.4745 time to fit residues: 343.2021 Evaluate side-chains 200 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.840 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 1.6328 time to fit residues: 5.7953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 16910 Z= 0.168 Angle : 0.582 9.815 23099 Z= 0.268 Chirality : 0.043 0.199 2572 Planarity : 0.005 0.051 2761 Dihedral : 12.581 89.810 2578 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.32 (0.20), residues: 1902 helix: 2.41 (0.17), residues: 955 sheet: 0.36 (0.33), residues: 209 loop : -1.10 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.707 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 28 residues processed: 207 average time/residue: 1.5112 time to fit residues: 344.1391 Evaluate side-chains 199 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16910 Z= 0.171 Angle : 0.583 9.886 23099 Z= 0.269 Chirality : 0.043 0.195 2572 Planarity : 0.005 0.050 2761 Dihedral : 12.494 89.753 2578 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.33 (0.20), residues: 1902 helix: 2.41 (0.17), residues: 955 sheet: 0.38 (0.33), residues: 209 loop : -1.08 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 169 time to evaluate : 1.926 Fit side-chains outliers start: 37 outliers final: 35 residues processed: 197 average time/residue: 1.5787 time to fit residues: 340.3453 Evaluate side-chains 203 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 28 residues processed: 7 average time/residue: 1.0091 time to fit residues: 11.2744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 129 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 164 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16910 Z= 0.213 Angle : 0.630 10.536 23099 Z= 0.291 Chirality : 0.044 0.192 2572 Planarity : 0.005 0.049 2761 Dihedral : 12.656 89.329 2578 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.24 (0.20), residues: 1902 helix: 2.29 (0.17), residues: 961 sheet: 0.39 (0.33), residues: 209 loop : -1.10 (0.21), residues: 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.861 Fit side-chains outliers start: 33 outliers final: 31 residues processed: 202 average time/residue: 1.5459 time to fit residues: 341.8696 Evaluate side-chains 199 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.2329 time to fit residues: 3.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 0.0470 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 16910 Z= 0.176 Angle : 0.595 9.848 23099 Z= 0.275 Chirality : 0.043 0.193 2572 Planarity : 0.005 0.051 2761 Dihedral : 12.398 89.785 2578 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.32 (0.20), residues: 1902 helix: 2.38 (0.17), residues: 955 sheet: 0.44 (0.33), residues: 209 loop : -1.08 (0.22), residues: 738 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 1.723 Fit side-chains outliers start: 36 outliers final: 31 residues processed: 196 average time/residue: 1.6339 time to fit residues: 351.6890 Evaluate side-chains 198 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.2914 time to fit residues: 3.6322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 146 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 128 optimal weight: 7.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.063575 restraints weight = 25984.296| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.98 r_work: 0.2712 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 16910 Z= 0.160 Angle : 0.568 9.598 23099 Z= 0.264 Chirality : 0.042 0.193 2572 Planarity : 0.005 0.054 2761 Dihedral : 11.884 89.737 2578 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.50 (0.20), residues: 1902 helix: 2.55 (0.17), residues: 947 sheet: 0.43 (0.32), residues: 225 loop : -0.99 (0.22), residues: 730 =============================================================================== Job complete usr+sys time: 6612.06 seconds wall clock time: 117 minutes 16.97 seconds (7036.97 seconds total)