Starting phenix.real_space_refine (version: dev) on Fri May 13 14:04:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/05_2022/6kph_0746_trim_updated.pdb" } resolution = 2.41 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= -0.011 sd= 0.366 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 62832 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "B" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "C" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "F" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "G" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "K" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "L" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 316, 'PCIS': 1} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAI': 1, ' MG': 2, '9TY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 21.89, per 1000 atoms: 0.35 Number of scatterers: 62832 At special positions: 0 Unit cell: (140.28, 140.28, 140.28, 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) S 120 16.00 P 24 15.00 Mg 24 11.99 O 5976 8.00 N 5160 7.00 C 20316 6.00 H 31212 1.00 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: 41.39 Conformation dependent library (CDL) restraints added in 4.0 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 24 sheets defined 55.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 109 through 112 No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 233 through 243 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'B' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 95 No H-bonds generated for 'chain 'B' and resid 92 through 95' Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 216 removed outlier: 3.880A pdb=" N TRP B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 233 through 243 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'C' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 216 removed outlier: 3.882A pdb=" N TRP C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 233 through 243 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'D' and resid 25 through 37 removed outlier: 4.063A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 95 No H-bonds generated for 'chain 'D' and resid 92 through 95' Processing helix chain 'D' and resid 109 through 112 No H-bonds generated for 'chain 'D' and resid 109 through 112' Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 217 removed outlier: 3.881A pdb=" N TRP D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.559A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 233 through 243 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'E' and resid 25 through 37 removed outlier: 4.063A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 57 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 136 through 142 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Proline residue: E 200 - end of helix Processing helix chain 'E' and resid 221 through 228 Processing helix chain 'E' and resid 233 through 243 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 287 through 298 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'F' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 136 through 142 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 184 through 217 removed outlier: 3.881A pdb=" N TRP F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Proline residue: F 200 - end of helix removed outlier: 3.559A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 228 Processing helix chain 'F' and resid 233 through 243 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 287 through 298 Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'G' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 57 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 95 No H-bonds generated for 'chain 'G' and resid 92 through 95' Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 136 through 142 Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 184 through 216 removed outlier: 3.882A pdb=" N TRP G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Proline residue: G 200 - end of helix Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 233 through 243 Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 269 through 284 Processing helix chain 'G' and resid 287 through 298 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'H' and resid 25 through 37 removed outlier: 4.063A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 57 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 95 No H-bonds generated for 'chain 'H' and resid 92 through 95' Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 136 through 142 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 233 through 243 Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 269 through 284 Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 314 through 325 Processing helix chain 'I' and resid 25 through 37 removed outlier: 4.063A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 57 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 95 No H-bonds generated for 'chain 'I' and resid 92 through 95' Processing helix chain 'I' and resid 109 through 112 No H-bonds generated for 'chain 'I' and resid 109 through 112' Processing helix chain 'I' and resid 136 through 142 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.880A pdb=" N TRP I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 200 - end of helix removed outlier: 3.558A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 233 through 243 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 255 through 267 Processing helix chain 'I' and resid 269 through 284 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'J' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 95 No H-bonds generated for 'chain 'J' and resid 92 through 95' Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 136 through 142 Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'J' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Proline residue: J 200 - end of helix Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 233 through 243 Processing helix chain 'J' and resid 248 through 252 Processing helix chain 'J' and resid 255 through 267 Processing helix chain 'J' and resid 269 through 284 Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 314 through 325 Processing helix chain 'K' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 95 No H-bonds generated for 'chain 'K' and resid 92 through 95' Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 136 through 142 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 233 through 243 Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 Processing helix chain 'K' and resid 269 through 284 Processing helix chain 'K' and resid 287 through 298 Processing helix chain 'K' and resid 301 through 311 Processing helix chain 'K' and resid 314 through 325 Processing helix chain 'L' and resid 25 through 37 removed outlier: 4.063A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 57 Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' Processing helix chain 'L' and resid 109 through 112 No H-bonds generated for 'chain 'L' and resid 109 through 112' Processing helix chain 'L' and resid 136 through 142 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 233 through 243 Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 255 through 267 Processing helix chain 'L' and resid 269 through 284 Processing helix chain 'L' and resid 287 through 298 Processing helix chain 'L' and resid 301 through 311 Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'K' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 179 through 181 removed outlier: 6.965A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 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: 19.03 Time building geometry restraints manager: 43.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 31199 1.03 - 1.22: 25 1.22 - 1.41: 13314 1.41 - 1.61: 18654 1.61 - 1.80: 300 Bond restraints: 63492 Sorted by residual: bond pdb=" C1B NAI D 403 " pdb=" C2B NAI D 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI I 403 " pdb=" C2B NAI I 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI C 403 " pdb=" C2B NAI C 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI H 403 " pdb=" C2B NAI H 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI L 403 " pdb=" C2B NAI L 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 63487 not shown) Histogram of bond angle deviations from ideal: 59.76 - 74.66: 47 74.66 - 89.55: 262 89.55 - 104.45: 411 104.45 - 119.35: 88288 119.35 - 134.25: 25988 Bond angle restraints: 114996 Sorted by residual: angle pdb=" CG1 VAL H 46 " pdb=" CB VAL H 46 " pdb=" HB VAL H 46 " ideal model delta sigma weight residual 108.00 69.66 38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" CG2 VAL H 46 " pdb=" CB VAL H 46 " pdb=" HB VAL H 46 " ideal model delta sigma weight residual 108.00 71.60 36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" OG1 THR I 17 " pdb=" CB THR I 17 " pdb=" HB THR I 17 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" OG1 THR K 17 " pdb=" CB THR K 17 " pdb=" HB THR K 17 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" OG1 THR G 17 " pdb=" CB THR G 17 " pdb=" HB THR G 17 " ideal model delta sigma weight residual 109.00 73.43 35.57 3.00e+00 1.11e-01 1.41e+02 ... (remaining 114991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.43: 24160 29.43 - 58.87: 757 58.87 - 88.30: 79 88.30 - 117.73: 0 117.73 - 147.17: 12 Dihedral angle restraints: 25008 sinusoidal: 11652 harmonic: 13356 Sorted by residual: dihedral pdb=" C02 9TY E 404 " pdb=" C03 9TY E 404 " pdb=" C08 9TY E 404 " pdb=" C07 9TY E 404 " ideal model delta sinusoidal sigma weight residual 253.97 106.80 147.17 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C02 9TY F 404 " pdb=" C03 9TY F 404 " pdb=" C08 9TY F 404 " pdb=" C07 9TY F 404 " ideal model delta sinusoidal sigma weight residual 253.97 106.81 147.16 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C02 9TY K 404 " pdb=" C03 9TY K 404 " pdb=" C08 9TY K 404 " pdb=" C07 9TY K 404 " ideal model delta sinusoidal sigma weight residual 253.97 106.83 147.14 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 25005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 4728 0.347 - 0.694: 0 0.694 - 1.040: 0 1.040 - 1.387: 0 1.387 - 1.734: 36 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CG LEU I 75 " pdb=" CB LEU I 75 " pdb=" CD1 LEU I 75 " pdb=" CD2 LEU I 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU D 75 " pdb=" CB LEU D 75 " pdb=" CD1 LEU D 75 " pdb=" CD2 LEU D 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU E 75 " pdb=" CB LEU E 75 " pdb=" CD1 LEU E 75 " pdb=" CD2 LEU E 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 ... (remaining 4761 not shown) Planarity restraints: 9264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 284 " -0.006 2.00e-02 2.50e+03 7.30e-03 2.13e+00 pdb=" CG TRP G 284 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP G 284 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP G 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 284 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 284 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 284 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 284 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 284 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 284 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP G 284 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP G 284 " 0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP G 284 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 284 " -0.011 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP G 284 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 284 " -0.006 2.00e-02 2.50e+03 7.07e-03 2.00e+00 pdb=" CG TRP L 284 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 284 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 284 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 284 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 284 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 284 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP L 284 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP L 284 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP L 284 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 284 " -0.010 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP L 284 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 284 " -0.006 2.00e-02 2.50e+03 6.73e-03 1.81e+00 pdb=" CG TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP D 284 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP D 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 284 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 284 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 284 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 284 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 284 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 284 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP D 284 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP D 284 " 0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 284 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP D 284 " -0.002 2.00e-02 2.50e+03 ... (remaining 9261 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3042 2.15 - 2.77: 123403 2.77 - 3.38: 172303 3.38 - 3.99: 229560 3.99 - 4.60: 373570 Nonbonded interactions: 901878 Sorted by model distance: nonbonded pdb=" O MET A 193 " pdb=" HG1 THR A 197 " model vdw 1.543 1.850 nonbonded pdb=" O MET G 193 " pdb=" HG1 THR G 197 " model vdw 1.545 1.850 nonbonded pdb=" O MET D 193 " pdb=" HG1 THR D 197 " model vdw 1.545 1.850 nonbonded pdb=" O MET K 193 " pdb=" HG1 THR K 197 " model vdw 1.546 1.850 nonbonded pdb=" O MET J 193 " pdb=" HG1 THR J 197 " model vdw 1.546 1.850 ... (remaining 901873 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20316 2.51 5 N 5160 2.21 5 O 5976 1.98 5 H 31212 0.53 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: 1.370 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: 0.710 Extract box with map and model: 12.920 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.420 Process input model: 147.350 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.014 0.241 32280 Z= 0.879 Angle : 1.012 13.401 43704 Z= 0.474 Chirality : 0.147 1.734 4764 Planarity : 0.004 0.033 5484 Dihedral : 14.011 147.165 11904 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.25 (0.10), residues: 3912 helix: -2.16 (0.08), residues: 2292 sheet: -2.31 (0.21), residues: 456 loop : -4.07 (0.14), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 4.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 721 average time/residue: 3.1673 time to fit residues: 2609.8521 Evaluate side-chains 355 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 353 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.7408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 45 ASN A 96 GLN A 110 ASN A 278 ASN B 25 ASN B 45 ASN B 96 GLN B 110 ASN B 278 ASN C 25 ASN C 45 ASN C 96 GLN C 110 ASN C 278 ASN D 25 ASN D 45 ASN D 96 GLN D 110 ASN D 278 ASN E 25 ASN E 45 ASN E 96 GLN E 110 ASN E 278 ASN F 25 ASN F 45 ASN F 96 GLN F 110 ASN F 278 ASN G 25 ASN G 45 ASN G 96 GLN G 110 ASN G 278 ASN H 25 ASN H 45 ASN H 96 GLN H 110 ASN H 278 ASN I 25 ASN ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 96 GLN I 110 ASN I 278 ASN J 25 ASN J 45 ASN J 96 GLN J 110 ASN ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 ASN K 25 ASN K 45 ASN K 96 GLN K 110 ASN K 278 ASN L 25 ASN L 45 ASN L 96 GLN L 110 ASN L 142 GLN L 278 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 32280 Z= 0.247 Angle : 0.731 12.117 43704 Z= 0.369 Chirality : 0.150 1.696 4764 Planarity : 0.005 0.077 5484 Dihedral : 9.987 147.208 4452 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.00 (0.12), residues: 3912 helix: -0.18 (0.10), residues: 2292 sheet: 0.07 (0.35), residues: 180 loop : -3.49 (0.13), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 388 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 29 residues processed: 432 average time/residue: 2.5177 time to fit residues: 1290.7795 Evaluate side-chains 352 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 323 time to evaluate : 3.934 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 1.0093 time to fit residues: 19.3914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.043 32280 Z= 0.430 Angle : 0.753 11.415 43704 Z= 0.390 Chirality : 0.149 1.730 4764 Planarity : 0.005 0.070 5484 Dihedral : 9.554 146.885 4452 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.49 (0.13), residues: 3912 helix: -0.01 (0.10), residues: 2400 sheet: -1.48 (0.23), residues: 456 loop : -2.89 (0.17), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 319 time to evaluate : 4.892 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: 70 outliers final: 41 residues processed: 360 average time/residue: 2.5606 time to fit residues: 1101.3592 Evaluate side-chains 320 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 4.161 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 19 residues processed: 22 average time/residue: 1.2950 time to fit residues: 43.7485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 1.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 350 optimal weight: 0.6980 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 HIS ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 HIS ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 HIS ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 32280 Z= 0.240 Angle : 0.678 11.419 43704 Z= 0.345 Chirality : 0.148 1.686 4764 Planarity : 0.003 0.078 5484 Dihedral : 9.400 147.125 4452 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.90 (0.13), residues: 3912 helix: 0.50 (0.10), residues: 2400 sheet: -0.72 (0.26), residues: 324 loop : -2.84 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 344 time to evaluate : 4.955 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: 59 outliers final: 26 residues processed: 379 average time/residue: 2.6831 time to fit residues: 1203.1671 Evaluate side-chains 328 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 302 time to evaluate : 3.969 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.7467 time to fit residues: 11.2211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 32280 Z= 0.281 Angle : 0.689 11.411 43704 Z= 0.350 Chirality : 0.149 1.700 4764 Planarity : 0.004 0.085 5484 Dihedral : 9.349 147.011 4452 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.65 (0.13), residues: 3912 helix: 0.69 (0.10), residues: 2400 sheet: -0.52 (0.27), residues: 324 loop : -2.77 (0.17), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 313 time to evaluate : 4.004 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 outliers start: 61 outliers final: 29 residues processed: 352 average time/residue: 2.6812 time to fit residues: 1112.1614 Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 4.014 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 0.9881 time to fit residues: 19.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 32280 Z= 0.250 Angle : 0.680 11.501 43704 Z= 0.344 Chirality : 0.149 1.692 4764 Planarity : 0.003 0.080 5484 Dihedral : 9.278 147.112 4452 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.42 (0.13), residues: 3912 helix: 0.88 (0.10), residues: 2400 sheet: -0.33 (0.27), residues: 324 loop : -2.71 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 323 time to evaluate : 4.006 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: 53 outliers final: 31 residues processed: 348 average time/residue: 2.7483 time to fit residues: 1128.8711 Evaluate side-chains 344 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 313 time to evaluate : 3.952 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 12 average time/residue: 0.7639 time to fit residues: 19.6703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 32280 Z= 0.252 Angle : 0.679 12.274 43704 Z= 0.343 Chirality : 0.149 1.695 4764 Planarity : 0.004 0.102 5484 Dihedral : 9.249 147.091 4452 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.27 (0.13), residues: 3912 helix: 0.98 (0.10), residues: 2400 sheet: -0.24 (0.27), residues: 324 loop : -2.62 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 324 time to evaluate : 4.213 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 outliers start: 52 outliers final: 35 residues processed: 350 average time/residue: 2.7445 time to fit residues: 1139.1930 Evaluate side-chains 337 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 3.991 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 20 residues processed: 16 average time/residue: 1.2398 time to fit residues: 33.3229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 32280 Z= 0.265 Angle : 0.693 12.309 43704 Z= 0.350 Chirality : 0.150 1.696 4764 Planarity : 0.003 0.107 5484 Dihedral : 9.241 147.061 4452 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.21 (0.13), residues: 3912 helix: 1.01 (0.10), residues: 2400 sheet: -0.24 (0.27), residues: 324 loop : -2.55 (0.16), residues: 1188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 317 time to evaluate : 4.913 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: 50 outliers final: 37 residues processed: 340 average time/residue: 2.7177 time to fit residues: 1086.8469 Evaluate side-chains 336 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 299 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 20 residues processed: 18 average time/residue: 1.0561 time to fit residues: 32.0994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 0.0980 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 311 optimal weight: 0.8980 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 32280 Z= 0.174 Angle : 0.661 12.355 43704 Z= 0.327 Chirality : 0.149 1.690 4764 Planarity : 0.003 0.104 5484 Dihedral : 9.090 147.344 4452 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.28 (0.13), residues: 3912 helix: 1.36 (0.10), residues: 2424 sheet: -0.00 (0.27), residues: 324 loop : -2.36 (0.16), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 329 time to evaluate : 4.136 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: 27 outliers final: 19 residues processed: 349 average time/residue: 2.6360 time to fit residues: 1087.4448 Evaluate side-chains 334 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 315 time to evaluate : 3.941 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 1.3699 time to fit residues: 8.3899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 8.9990 chunk 364 optimal weight: 4.9990 chunk 222 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 0.0060 chunk 304 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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: 0.8505 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 32280 Z= 0.231 Angle : 0.687 11.655 43704 Z= 0.344 Chirality : 0.149 1.698 4764 Planarity : 0.003 0.104 5484 Dihedral : 9.090 147.118 4452 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.22 (0.13), residues: 3912 helix: 1.31 (0.10), residues: 2424 sheet: -0.01 (0.27), residues: 324 loop : -2.37 (0.16), residues: 1164 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 314 time to evaluate : 4.174 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: 24 outliers final: 18 residues processed: 331 average time/residue: 2.6958 time to fit residues: 1048.5794 Evaluate side-chains 317 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 299 time to evaluate : 3.920 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.6336 time to fit residues: 5.7851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 0.6980 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.101452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073883 restraints weight = 193204.167| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.67 r_work: 0.2895 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.2865 rms_B_bonded: 2.44 restraints_weight: 0.1250 r_work: 0.2850 rms_B_bonded: 2.53 restraints_weight: 0.0625 r_work: 0.2834 rms_B_bonded: 2.66 restraints_weight: 0.0312 r_work: 0.2818 rms_B_bonded: 2.83 restraints_weight: 0.0156 r_work: 0.2801 rms_B_bonded: 3.04 restraints_weight: 0.0078 r_work: 0.2782 rms_B_bonded: 3.30 restraints_weight: 0.0039 r_work: 0.2763 rms_B_bonded: 3.61 restraints_weight: 0.0020 r_work: 0.2742 rms_B_bonded: 3.97 restraints_weight: 0.0010 r_work: 0.2720 rms_B_bonded: 4.40 restraints_weight: 0.0005 r_work: 0.2697 rms_B_bonded: 4.89 restraints_weight: 0.0002 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 32280 Z= 0.251 Angle : 0.692 12.231 43704 Z= 0.347 Chirality : 0.150 1.687 4764 Planarity : 0.004 0.118 5484 Dihedral : 9.152 147.131 4452 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.19 (0.13), residues: 3912 helix: 1.29 (0.10), residues: 2424 sheet: -0.04 (0.27), residues: 324 loop : -2.37 (0.16), residues: 1164 =============================================================================== Job complete usr+sys time: 17994.03 seconds wall clock time: 309 minutes 42.89 seconds (18582.89 seconds total)