Starting phenix.real_space_refine (version: dev) on Wed Feb 22 01:13:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2023/7cr7_30448_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 84": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 84": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "G GLU 140": "OE1" <-> "OE2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G GLU 257": "OE1" <-> "OE2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16136 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "F" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "C" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "G" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2886 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 7, 'TRANS': 346} Chain breaks: 2 Chain: "H" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1126 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'FBX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.71, per 1000 atoms: 0.54 Number of scatterers: 16136 At special positions: 0 Unit cell: (130.806, 130.806, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 F 4 9.00 O 2912 8.00 N 2748 7.00 C 10384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 2.5 seconds 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 8 sheets defined 76.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 92 through 114 removed outlier: 4.031A pdb=" N THR A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 150 removed outlier: 4.568A pdb=" N ILE A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 removed outlier: 4.103A pdb=" N ALA A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 216 through 252 removed outlier: 5.447A pdb=" N LYS A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 275 Processing helix chain 'A' and resid 288 through 349 removed outlier: 3.867A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.901A pdb=" N PHE A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Proline residue: A 335 - end of helix removed outlier: 3.943A pdb=" N ILE A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 536 through 557 Processing helix chain 'A' and resid 563 through 598 Proline residue: A 597 - end of helix Processing helix chain 'F' and resid 7 through 20 Processing helix chain 'F' and resid 30 through 40 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 66 through 74 Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'F' and resid 83 through 93 removed outlier: 4.607A pdb=" N PHE F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 92 through 114 removed outlier: 4.032A pdb=" N THR B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 150 removed outlier: 4.567A pdb=" N ILE B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS B 150 " --> pdb=" O TRP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 165 removed outlier: 4.103A pdb=" N ALA B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 216 through 252 removed outlier: 5.447A pdb=" N LYS B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 275 Processing helix chain 'B' and resid 288 through 349 removed outlier: 3.867A pdb=" N THR B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Proline residue: B 308 - end of helix removed outlier: 3.901A pdb=" N PHE B 329 " --> pdb=" O ARG B 325 " (cutoff:3.500A) Proline residue: B 335 - end of helix removed outlier: 3.944A pdb=" N ILE B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 536 through 557 Processing helix chain 'B' and resid 563 through 598 Proline residue: B 597 - end of helix Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 66 through 74 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 93 removed outlier: 4.605A pdb=" N PHE C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 119 through 129 Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 92 through 114 removed outlier: 4.032A pdb=" N THR D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 150 removed outlier: 4.568A pdb=" N ILE D 128 " --> pdb=" O GLY D 124 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY D 149 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS D 150 " --> pdb=" O TRP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 165 removed outlier: 4.102A pdb=" N ALA D 164 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 216 through 252 removed outlier: 5.446A pdb=" N LYS D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 275 Processing helix chain 'D' and resid 288 through 349 removed outlier: 3.867A pdb=" N THR D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Proline residue: D 308 - end of helix removed outlier: 3.902A pdb=" N PHE D 329 " --> pdb=" O ARG D 325 " (cutoff:3.500A) Proline residue: D 335 - end of helix removed outlier: 3.944A pdb=" N ILE D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 536 through 557 Processing helix chain 'D' and resid 563 through 598 Proline residue: D 597 - end of helix Processing helix chain 'E' and resid 7 through 20 Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 66 through 74 Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 83 through 93 removed outlier: 4.606A pdb=" N PHE E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 119 through 129 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 92 through 114 removed outlier: 4.031A pdb=" N THR G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 150 removed outlier: 4.568A pdb=" N ILE G 128 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS G 150 " --> pdb=" O TRP G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 165 removed outlier: 4.102A pdb=" N ALA G 164 " --> pdb=" O ARG G 160 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG G 165 " --> pdb=" O LEU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 197 through 211 Processing helix chain 'G' and resid 216 through 252 removed outlier: 5.447A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 275 Processing helix chain 'G' and resid 288 through 349 removed outlier: 3.867A pdb=" N THR G 296 " --> pdb=" O LEU G 292 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU G 299 " --> pdb=" O ALA G 295 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Proline residue: G 308 - end of helix removed outlier: 3.901A pdb=" N PHE G 329 " --> pdb=" O ARG G 325 " (cutoff:3.500A) Proline residue: G 335 - end of helix removed outlier: 3.944A pdb=" N ILE G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN G 341 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR G 349 " --> pdb=" O ARG G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 355 No H-bonds generated for 'chain 'G' and resid 353 through 355' Processing helix chain 'G' and resid 357 through 366 Processing helix chain 'G' and resid 536 through 557 Processing helix chain 'G' and resid 563 through 598 Proline residue: G 597 - end of helix Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 30 through 40 Processing helix chain 'H' and resid 46 through 56 Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'H' and resid 83 through 93 removed outlier: 4.606A pdb=" N PHE H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 111 Processing helix chain 'H' and resid 119 through 129 Processing helix chain 'H' and resid 140 through 147 Processing sheet with id= A, first strand: chain 'F' and resid 27 through 29 Processing sheet with id= B, first strand: chain 'F' and resid 100 through 102 Processing sheet with id= C, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= D, first strand: chain 'C' and resid 100 through 102 Processing sheet with id= E, first strand: chain 'E' and resid 27 through 29 Processing sheet with id= F, first strand: chain 'E' and resid 100 through 102 Processing sheet with id= G, first strand: chain 'H' and resid 27 through 29 Processing sheet with id= H, first strand: chain 'H' and resid 100 through 102 1092 hydrogen bonds defined for protein. 3276 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: 5.72 Time building geometry restraints manager: 8.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2609 1.31 - 1.43: 4630 1.43 - 1.56: 9085 1.56 - 1.69: 4 1.69 - 1.81: 148 Bond restraints: 16476 Sorted by residual: bond pdb=" C17 FBX D1001 " pdb=" C19 FBX D1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C17 FBX A1001 " pdb=" C19 FBX A1001 " ideal model delta sigma weight residual 1.381 1.522 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C17 FBX B1001 " pdb=" C19 FBX B1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" C17 FBX G1001 " pdb=" C19 FBX G1001 " ideal model delta sigma weight residual 1.381 1.521 -0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 FBX A1001 " pdb=" C18 FBX A1001 " ideal model delta sigma weight residual 1.388 1.518 -0.130 2.00e-02 2.50e+03 4.23e+01 ... (remaining 16471 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.90: 310 106.90 - 113.68: 9214 113.68 - 120.45: 6879 120.45 - 127.23: 5673 127.23 - 134.00: 148 Bond angle restraints: 22224 Sorted by residual: angle pdb=" C LEU D 559 " pdb=" N ARG D 560 " pdb=" CA ARG D 560 " ideal model delta sigma weight residual 121.80 106.99 14.81 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU A 559 " pdb=" N ARG A 560 " pdb=" CA ARG A 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU G 559 " pdb=" N ARG G 560 " pdb=" CA ARG G 560 " ideal model delta sigma weight residual 121.80 107.00 14.80 2.44e+00 1.68e-01 3.68e+01 angle pdb=" C LEU B 559 " pdb=" N ARG B 560 " pdb=" CA ARG B 560 " ideal model delta sigma weight residual 121.80 107.04 14.76 2.44e+00 1.68e-01 3.66e+01 angle pdb=" CA PRO D 561 " pdb=" N PRO D 561 " pdb=" CD PRO D 561 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.54e+01 ... (remaining 22219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.74: 9445 32.74 - 65.47: 219 65.47 - 98.21: 20 98.21 - 130.94: 0 130.94 - 163.68: 4 Dihedral angle restraints: 9688 sinusoidal: 3936 harmonic: 5752 Sorted by residual: dihedral pdb=" C8 FBX D1001 " pdb=" C7 FBX D1001 " pdb=" N4 FBX D1001 " pdb=" C9 FBX D1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.22 -163.68 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX G1001 " pdb=" C7 FBX G1001 " pdb=" N4 FBX G1001 " pdb=" C9 FBX G1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.19 -163.65 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C8 FBX A1001 " pdb=" C7 FBX A1001 " pdb=" N4 FBX A1001 " pdb=" C9 FBX A1001 " ideal model delta sinusoidal sigma weight residual -75.46 88.17 -163.63 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 9685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1572 0.034 - 0.068: 630 0.068 - 0.102: 149 0.102 - 0.136: 72 0.136 - 0.169: 5 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CG LEU A 559 " pdb=" CB LEU A 559 " pdb=" CD1 LEU A 559 " pdb=" CD2 LEU A 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CG LEU G 559 " pdb=" CB LEU G 559 " pdb=" CD1 LEU G 559 " pdb=" CD2 LEU G 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CG LEU B 559 " pdb=" CB LEU B 559 " pdb=" CD1 LEU B 559 " pdb=" CD2 LEU B 559 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 2425 not shown) Planarity restraints: 2804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 560 " -0.042 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO D 561 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 561 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 561 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO G 561 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO G 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 561 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 560 " 0.042 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO A 561 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " 0.034 5.00e-02 4.00e+02 ... (remaining 2801 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 224 2.44 - 3.06: 14189 3.06 - 3.67: 27585 3.67 - 4.29: 41898 4.29 - 4.90: 60428 Nonbonded interactions: 144324 Sorted by model distance: nonbonded pdb=" O TYR G 562 " pdb=" N ASP G 566 " model vdw 1.825 2.520 nonbonded pdb=" O TYR A 562 " pdb=" N ASP A 566 " model vdw 1.826 2.520 nonbonded pdb=" O TYR D 562 " pdb=" N ASP D 566 " model vdw 1.826 2.520 nonbonded pdb=" O TYR B 562 " pdb=" N ASP B 566 " model vdw 1.826 2.520 nonbonded pdb=" O VAL D 111 " pdb=" OG1 THR D 114 " model vdw 1.962 2.440 ... (remaining 144319 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 'D' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } 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: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 10384 2.51 5 N 2748 2.21 5 O 2912 1.98 5 F 4 1.80 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.230 Process input model: 43.830 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.141 16476 Z= 0.537 Angle : 0.789 14.807 22224 Z= 0.440 Chirality : 0.041 0.169 2428 Planarity : 0.005 0.062 2804 Dihedral : 14.627 163.679 5992 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 92.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.57 % Favored : 94.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.15), residues: 1956 helix: -2.41 (0.10), residues: 1448 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.898 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 outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3552 time to fit residues: 189.3212 Evaluate side-chains 279 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 16476 Z= 0.268 Angle : 0.771 10.464 22224 Z= 0.400 Chirality : 0.043 0.174 2428 Planarity : 0.005 0.054 2804 Dihedral : 9.026 151.240 2216 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 1956 helix: -0.35 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -2.02 (0.31), residues: 444 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 345 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 356 average time/residue: 0.3304 time to fit residues: 166.4243 Evaluate side-chains 286 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 273 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1398 time to fit residues: 5.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 40.0000 chunk 143 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN B 96 HIS ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 16476 Z= 0.276 Angle : 0.722 11.776 22224 Z= 0.380 Chirality : 0.041 0.155 2428 Planarity : 0.005 0.070 2804 Dihedral : 8.948 151.164 2216 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.54 (0.19), residues: 1956 helix: 0.03 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -1.35 (0.33), residues: 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 305 time to evaluate : 1.940 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 outliers start: 28 outliers final: 11 residues processed: 324 average time/residue: 0.2952 time to fit residues: 139.5602 Evaluate side-chains 287 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 1.870 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1597 time to fit residues: 5.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 16476 Z= 0.242 Angle : 0.690 9.158 22224 Z= 0.363 Chirality : 0.040 0.202 2428 Planarity : 0.004 0.054 2804 Dihedral : 8.890 152.647 2216 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.17 (0.19), residues: 1956 helix: 0.32 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.38 (0.33), residues: 428 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 305 time to evaluate : 1.906 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: 30 outliers final: 15 residues processed: 321 average time/residue: 0.3070 time to fit residues: 141.7741 Evaluate side-chains 289 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 1.952 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1473 time to fit residues: 6.8052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN B 96 HIS B 204 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN G 78 GLN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 16476 Z= 0.246 Angle : 0.697 9.464 22224 Z= 0.366 Chirality : 0.040 0.155 2428 Planarity : 0.004 0.045 2804 Dihedral : 8.851 153.382 2216 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.03 (0.19), residues: 1956 helix: 0.48 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.33 (0.33), residues: 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 303 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 321 average time/residue: 0.2979 time to fit residues: 138.5373 Evaluate side-chains 287 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 276 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1516 time to fit residues: 5.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN E 50 GLN ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 16476 Z= 0.264 Angle : 0.739 9.980 22224 Z= 0.388 Chirality : 0.041 0.181 2428 Planarity : 0.004 0.046 2804 Dihedral : 8.909 155.149 2216 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.01 (0.19), residues: 1956 helix: 0.44 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -1.29 (0.32), residues: 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 293 time to evaluate : 1.868 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: 31 outliers final: 14 residues processed: 311 average time/residue: 0.3192 time to fit residues: 142.2243 Evaluate side-chains 290 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 276 time to evaluate : 1.876 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1553 time to fit residues: 6.5300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 chunk 108 optimal weight: 9.9990 chunk 138 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.6421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 16476 Z= 0.224 Angle : 0.745 9.450 22224 Z= 0.387 Chirality : 0.041 0.223 2428 Planarity : 0.004 0.058 2804 Dihedral : 8.969 158.315 2216 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.24 (0.19), residues: 1956 helix: 0.59 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.03 (0.33), residues: 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 311 average time/residue: 0.3225 time to fit residues: 142.4870 Evaluate side-chains 287 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1894 time to fit residues: 6.0607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 16476 Z= 0.289 Angle : 0.788 12.451 22224 Z= 0.413 Chirality : 0.043 0.187 2428 Planarity : 0.005 0.048 2804 Dihedral : 9.006 158.310 2216 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.19), residues: 1956 helix: 0.36 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.15 (0.32), residues: 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 290 average time/residue: 0.3361 time to fit residues: 140.2088 Evaluate side-chains 282 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 271 time to evaluate : 2.154 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1628 time to fit residues: 6.1151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 16476 Z= 0.232 Angle : 0.781 10.792 22224 Z= 0.407 Chirality : 0.042 0.204 2428 Planarity : 0.004 0.047 2804 Dihedral : 9.028 161.097 2216 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 0.02 (0.19), residues: 1956 helix: 0.44 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.22 (0.34), residues: 428 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 303 average time/residue: 0.3315 time to fit residues: 141.9799 Evaluate side-chains 289 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 279 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1457 time to fit residues: 5.4820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16476 Z= 0.246 Angle : 0.807 12.939 22224 Z= 0.424 Chirality : 0.044 0.230 2428 Planarity : 0.005 0.065 2804 Dihedral : 9.078 161.921 2216 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.04 (0.19), residues: 1956 helix: 0.44 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -1.19 (0.34), residues: 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3912 Ramachandran restraints generated. 1956 Oldfield, 0 Emsley, 1956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 288 time to evaluate : 1.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 291 average time/residue: 0.3381 time to fit residues: 139.0765 Evaluate side-chains 283 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 278 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1400 time to fit residues: 3.8400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 0.0670 chunk 47 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 9 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.181150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.139959 restraints weight = 44137.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.139732 restraints weight = 22803.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.140182 restraints weight = 16233.035| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 16476 Z= 0.258 Angle : 0.846 15.832 22224 Z= 0.436 Chirality : 0.044 0.249 2428 Planarity : 0.005 0.059 2804 Dihedral : 9.080 162.755 2216 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.01 (0.19), residues: 1956 helix: 0.42 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.26 (0.34), residues: 428 =============================================================================== Job complete usr+sys time: 3286.65 seconds wall clock time: 61 minutes 26.19 seconds (3686.19 seconds total)