Starting phenix.real_space_refine on Fri Feb 16 18:49:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2024/7cr7_30448_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2024/7cr7_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_2024/7cr7_30448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2024/7cr7_30448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2024/7cr7_30448_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cr7_30448/02_2024/7cr7_30448_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 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. 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-5238/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: 8.65, 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: 6.95 Conformation dependent library (CDL) restraints added in 2.6 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: 2.58 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: 4.81 Time building geometry restraints manager: 7.51 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 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: 0.010 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.720 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 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 % Allowed : 3.55 % Favored : 96.45 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 360 HIS 0.004 0.002 HIS G 96 PHE 0.026 0.002 PHE F 142 TYR 0.024 0.003 TYR G 280 ARG 0.005 0.001 ARG G 353 *********************** 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 : 1.921 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: A 171 ILE cc_start: 0.8347 (mm) cc_final: 0.8081 (mm) REVERT: A 266 ASP cc_start: 0.7527 (m-30) cc_final: 0.7247 (m-30) REVERT: F 13 PHE cc_start: 0.3397 (m-10) cc_final: 0.2516 (m-80) REVERT: F 73 MET cc_start: 0.5989 (mmm) cc_final: 0.5524 (mmp) REVERT: B 101 LEU cc_start: 0.8987 (mt) cc_final: 0.8777 (mt) REVERT: B 171 ILE cc_start: 0.8231 (mm) cc_final: 0.7965 (mm) REVERT: B 546 MET cc_start: 0.7897 (tpt) cc_final: 0.7679 (tpp) REVERT: C 54 ASN cc_start: 0.7734 (m-40) cc_final: 0.7526 (t0) REVERT: D 171 ILE cc_start: 0.8289 (mm) cc_final: 0.7974 (mm) REVERT: D 266 ASP cc_start: 0.7372 (m-30) cc_final: 0.7074 (m-30) REVERT: E 13 PHE cc_start: 0.3195 (m-10) cc_final: 0.2326 (m-80) REVERT: E 76 LYS cc_start: 0.6609 (mttt) cc_final: 0.6375 (tptt) REVERT: G 171 ILE cc_start: 0.8303 (mm) cc_final: 0.8006 (mm) REVERT: G 546 MET cc_start: 0.8035 (tpt) cc_final: 0.7801 (tpp) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.3585 time to fit residues: 191.4576 Evaluate side-chains 281 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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: 9.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 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: 0.6872 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16476 Z= 0.274 Angle : 0.771 10.487 22224 Z= 0.400 Chirality : 0.043 0.168 2428 Planarity : 0.005 0.054 2804 Dihedral : 8.988 150.917 2216 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.95 % Allowed : 12.53 % Favored : 85.52 % 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: -1.20 (0.18), residues: 1956 helix: -0.32 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -2.05 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 288 HIS 0.004 0.001 HIS A 324 PHE 0.020 0.002 PHE F 142 TYR 0.021 0.003 TYR A 280 ARG 0.006 0.001 ARG D 333 *********************** 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: 33 poor density : 348 time to evaluate : 1.775 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: A 171 ILE cc_start: 0.8239 (mm) cc_final: 0.7989 (mm) REVERT: A 209 ILE cc_start: 0.9235 (mt) cc_final: 0.8962 (mt) REVERT: A 211 MET cc_start: 0.7232 (tmm) cc_final: 0.6996 (tmm) REVERT: A 546 MET cc_start: 0.7668 (tpp) cc_final: 0.7434 (tpp) REVERT: F 126 ILE cc_start: 0.6920 (mm) cc_final: 0.6668 (mm) REVERT: B 171 ILE cc_start: 0.8153 (mm) cc_final: 0.7864 (mm) REVERT: B 211 MET cc_start: 0.7326 (tmm) cc_final: 0.7082 (tmm) REVERT: C 13 PHE cc_start: 0.2658 (m-10) cc_final: 0.2241 (m-10) REVERT: C 52 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7259 (tmm) REVERT: D 171 ILE cc_start: 0.8169 (mm) cc_final: 0.7899 (mm) REVERT: D 209 ILE cc_start: 0.9237 (mt) cc_final: 0.8972 (mt) REVERT: E 52 MET cc_start: 0.7678 (tmm) cc_final: 0.7408 (tmm) REVERT: E 76 LYS cc_start: 0.6674 (mttt) cc_final: 0.6304 (tptt) REVERT: E 126 ILE cc_start: 0.7080 (mm) cc_final: 0.6777 (mm) REVERT: G 171 ILE cc_start: 0.8317 (mm) cc_final: 0.8055 (mm) REVERT: G 209 ILE cc_start: 0.9298 (mt) cc_final: 0.9041 (mt) REVERT: H 52 MET cc_start: 0.7844 (tmm) cc_final: 0.7475 (tmm) REVERT: H 77 MET cc_start: 0.1362 (ptm) cc_final: 0.1150 (ptm) REVERT: H 126 ILE cc_start: 0.6971 (mm) cc_final: 0.6628 (mm) outliers start: 33 outliers final: 13 residues processed: 359 average time/residue: 0.3186 time to fit residues: 162.1575 Evaluate side-chains 292 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 278 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 360 TRP Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 0.2980 chunk 192 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 143 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16476 Z= 0.222 Angle : 0.697 12.378 22224 Z= 0.360 Chirality : 0.040 0.161 2428 Planarity : 0.004 0.051 2804 Dihedral : 8.938 154.485 2216 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.19 % Allowed : 15.01 % Favored : 82.80 % 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: -0.25 (0.19), residues: 1956 helix: 0.24 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.24 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 344 HIS 0.004 0.001 HIS D 575 PHE 0.040 0.002 PHE D 346 TYR 0.038 0.002 TYR D 363 ARG 0.011 0.001 ARG H 75 *********************** 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 373 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 336 time to evaluate : 1.977 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: A 171 ILE cc_start: 0.8216 (mm) cc_final: 0.8007 (mm) REVERT: A 546 MET cc_start: 0.7489 (tpp) cc_final: 0.7212 (tpp) REVERT: A 579 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8432 (tp) REVERT: F 126 ILE cc_start: 0.6949 (mm) cc_final: 0.6618 (mm) REVERT: B 96 HIS cc_start: 0.6718 (m-70) cc_final: 0.6398 (m-70) REVERT: B 171 ILE cc_start: 0.8164 (mm) cc_final: 0.7917 (mm) REVERT: D 171 ILE cc_start: 0.8314 (mm) cc_final: 0.8073 (mm) REVERT: E 125 MET cc_start: 0.5402 (tmm) cc_final: 0.5094 (ptm) REVERT: E 126 ILE cc_start: 0.7133 (mm) cc_final: 0.6494 (mm) REVERT: G 171 ILE cc_start: 0.8246 (mm) cc_final: 0.8007 (mm) REVERT: H 73 MET cc_start: 0.6441 (mmm) cc_final: 0.6118 (mtt) REVERT: H 126 ILE cc_start: 0.6999 (mm) cc_final: 0.6624 (mm) outliers start: 37 outliers final: 12 residues processed: 355 average time/residue: 0.2937 time to fit residues: 150.5803 Evaluate side-chains 311 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 298 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 546 MET Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 546 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 119 optimal weight: 0.6980 chunk 178 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16476 Z= 0.229 Angle : 0.680 9.640 22224 Z= 0.358 Chirality : 0.039 0.175 2428 Planarity : 0.004 0.048 2804 Dihedral : 8.797 152.938 2216 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.42 % Allowed : 17.67 % Favored : 79.91 % 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: 0.07 (0.19), residues: 1956 helix: 0.42 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -0.94 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 344 HIS 0.007 0.001 HIS A 575 PHE 0.024 0.002 PHE A 548 TYR 0.026 0.002 TYR D 363 ARG 0.010 0.001 ARG D 541 *********************** 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 355 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 314 time to evaluate : 2.000 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: A 130 GLU cc_start: 0.6976 (pt0) cc_final: 0.6609 (pp20) REVERT: A 546 MET cc_start: 0.7665 (tpp) cc_final: 0.7267 (tpp) REVERT: F 76 LYS cc_start: 0.3782 (tptt) cc_final: 0.3496 (tptp) REVERT: F 126 ILE cc_start: 0.6703 (mm) cc_final: 0.6369 (mm) REVERT: B 96 HIS cc_start: 0.6723 (m-70) cc_final: 0.6435 (m-70) REVERT: C 37 MET cc_start: 0.6668 (mmm) cc_final: 0.5509 (mmm) REVERT: D 130 GLU cc_start: 0.6716 (pt0) cc_final: 0.6351 (pp20) REVERT: E 101 ILE cc_start: 0.3428 (OUTLIER) cc_final: 0.3217 (tp) REVERT: E 126 ILE cc_start: 0.6948 (mm) cc_final: 0.6635 (mm) REVERT: G 130 GLU cc_start: 0.6617 (pt0) cc_final: 0.6283 (pp20) REVERT: H 50 GLN cc_start: 0.8180 (mm110) cc_final: 0.7914 (mm-40) REVERT: H 76 LYS cc_start: 0.2694 (tptt) cc_final: 0.2382 (tmtt) REVERT: H 126 ILE cc_start: 0.6958 (mm) cc_final: 0.6618 (mm) outliers start: 41 outliers final: 24 residues processed: 334 average time/residue: 0.3042 time to fit residues: 145.8400 Evaluate side-chains 318 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 293 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 351 LEU Chi-restraints excluded: chain H residue 90 PHE 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: 2.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16476 Z= 0.297 Angle : 0.721 9.534 22224 Z= 0.379 Chirality : 0.041 0.160 2428 Planarity : 0.005 0.059 2804 Dihedral : 8.766 150.919 2216 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.25 % Allowed : 18.85 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.36 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 344 HIS 0.006 0.001 HIS A 575 PHE 0.021 0.002 PHE D 297 TYR 0.020 0.002 TYR D 363 ARG 0.007 0.001 ARG D 207 *********************** 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 355 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 1.798 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: A 130 GLU cc_start: 0.6720 (pt0) cc_final: 0.6415 (pp20) REVERT: F 52 MET cc_start: 0.7607 (ppp) cc_final: 0.7196 (ppp) REVERT: F 76 LYS cc_start: 0.4606 (tptt) cc_final: 0.3785 (tmtt) REVERT: F 125 MET cc_start: 0.5151 (tmm) cc_final: 0.4332 (ptm) REVERT: F 126 ILE cc_start: 0.6973 (mm) cc_final: 0.6098 (mm) REVERT: B 96 HIS cc_start: 0.6873 (m-70) cc_final: 0.6559 (m-70) REVERT: C 13 PHE cc_start: 0.2188 (m-10) cc_final: 0.1561 (m-10) REVERT: C 73 MET cc_start: 0.6798 (mmm) cc_final: 0.6565 (mmm) REVERT: C 125 MET cc_start: 0.5983 (tmm) cc_final: 0.5515 (ppp) REVERT: C 145 MET cc_start: 0.4618 (ptt) cc_final: 0.4382 (ptm) REVERT: C 146 MET cc_start: 0.4676 (mmm) cc_final: 0.4226 (mmm) REVERT: D 130 GLU cc_start: 0.6767 (pt0) cc_final: 0.6298 (pp20) REVERT: D 252 LEU cc_start: 0.8274 (mt) cc_final: 0.8070 (mt) REVERT: E 125 MET cc_start: 0.5463 (tmm) cc_final: 0.5112 (ptm) REVERT: E 126 ILE cc_start: 0.7304 (mm) cc_final: 0.6619 (mm) REVERT: G 130 GLU cc_start: 0.6804 (pt0) cc_final: 0.6336 (pp20) REVERT: H 76 LYS cc_start: 0.2577 (tptt) cc_final: 0.2260 (tmtt) REVERT: H 101 ILE cc_start: 0.3372 (OUTLIER) cc_final: 0.3138 (tt) REVERT: H 126 ILE cc_start: 0.7094 (mm) cc_final: 0.6769 (mm) outliers start: 55 outliers final: 34 residues processed: 330 average time/residue: 0.3003 time to fit residues: 142.2857 Evaluate side-chains 321 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 286 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 546 MET Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 266 ASP Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 101 ILE 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: 0.7980 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 189 optimal weight: 0.1980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16476 Z= 0.225 Angle : 0.711 8.454 22224 Z= 0.370 Chirality : 0.040 0.229 2428 Planarity : 0.004 0.052 2804 Dihedral : 8.871 156.202 2216 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.36 % Allowed : 20.09 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.14 (0.19), residues: 1956 helix: 0.55 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -1.25 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 344 HIS 0.005 0.001 HIS A 575 PHE 0.030 0.002 PHE D 297 TYR 0.018 0.002 TYR D 363 ARG 0.013 0.001 ARG A 547 *********************** 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 347 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 307 time to evaluate : 1.753 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: A 96 HIS cc_start: 0.6749 (m-70) cc_final: 0.6453 (m-70) REVERT: A 130 GLU cc_start: 0.6828 (pt0) cc_final: 0.6309 (pp20) REVERT: F 76 LYS cc_start: 0.4289 (tptt) cc_final: 0.3867 (tmtt) REVERT: F 125 MET cc_start: 0.5392 (tmm) cc_final: 0.4710 (ptm) REVERT: F 126 ILE cc_start: 0.6808 (mm) cc_final: 0.5971 (mm) REVERT: B 96 HIS cc_start: 0.6695 (m-70) cc_final: 0.6470 (m-70) REVERT: B 145 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8898 (pt) REVERT: C 13 PHE cc_start: 0.2165 (m-10) cc_final: 0.1618 (m-10) REVERT: C 73 MET cc_start: 0.6886 (mmm) cc_final: 0.6374 (mmm) REVERT: D 130 GLU cc_start: 0.6760 (pt0) cc_final: 0.6328 (pp20) REVERT: D 145 ILE cc_start: 0.8981 (tp) cc_final: 0.8600 (pt) REVERT: E 125 MET cc_start: 0.5387 (tmm) cc_final: 0.4976 (ptm) REVERT: E 126 ILE cc_start: 0.7069 (mm) cc_final: 0.6405 (mm) REVERT: G 130 GLU cc_start: 0.6797 (pt0) cc_final: 0.6321 (pp20) REVERT: G 145 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8716 (pt) REVERT: H 126 ILE cc_start: 0.7200 (mm) cc_final: 0.6917 (mm) outliers start: 40 outliers final: 29 residues processed: 326 average time/residue: 0.3187 time to fit residues: 146.8842 Evaluate side-chains 318 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 323 GLN Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain H residue 90 PHE 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: 2.9990 chunk 108 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16476 Z= 0.303 Angle : 0.761 10.835 22224 Z= 0.399 Chirality : 0.042 0.189 2428 Planarity : 0.005 0.057 2804 Dihedral : 8.931 156.286 2216 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.19 % Allowed : 20.04 % Favored : 76.77 % 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: -0.22 (0.19), residues: 1956 helix: 0.25 (0.13), residues: 1540 sheet: None (None), residues: 0 loop : -1.25 (0.33), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 344 HIS 0.006 0.001 HIS A 575 PHE 0.036 0.002 PHE D 297 TYR 0.028 0.002 TYR B 118 ARG 0.007 0.001 ARG D 581 *********************** 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 343 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 289 time to evaluate : 1.782 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: A 96 HIS cc_start: 0.6822 (m-70) cc_final: 0.6529 (m-70) REVERT: A 130 GLU cc_start: 0.7019 (pt0) cc_final: 0.6430 (pp20) REVERT: F 73 MET cc_start: 0.6440 (mmm) cc_final: 0.5990 (mmm) REVERT: F 76 LYS cc_start: 0.4428 (tptt) cc_final: 0.3921 (tmtt) REVERT: F 126 ILE cc_start: 0.7059 (mm) cc_final: 0.6781 (mm) REVERT: B 96 HIS cc_start: 0.6870 (m-70) cc_final: 0.6621 (m-70) REVERT: B 145 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8867 (pt) REVERT: C 13 PHE cc_start: 0.2198 (m-10) cc_final: 0.1638 (m-10) REVERT: C 73 MET cc_start: 0.6533 (mmm) cc_final: 0.6200 (mmm) REVERT: C 125 MET cc_start: 0.5865 (tmm) cc_final: 0.5324 (ppp) REVERT: D 130 GLU cc_start: 0.6995 (pt0) cc_final: 0.6167 (pp20) REVERT: D 145 ILE cc_start: 0.9016 (tp) cc_final: 0.8669 (pt) REVERT: D 252 LEU cc_start: 0.8226 (mt) cc_final: 0.8022 (mt) REVERT: E 76 LYS cc_start: 0.5325 (tptt) cc_final: 0.4790 (tmtt) REVERT: E 77 MET cc_start: 0.1487 (ptt) cc_final: 0.1087 (ptt) REVERT: E 126 ILE cc_start: 0.7258 (mm) cc_final: 0.6967 (mm) REVERT: G 96 HIS cc_start: 0.6880 (m-70) cc_final: 0.6536 (m-70) REVERT: G 130 GLU cc_start: 0.6800 (pt0) cc_final: 0.6183 (pp20) REVERT: G 145 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8722 (pt) REVERT: H 126 ILE cc_start: 0.7366 (mm) cc_final: 0.7078 (mm) outliers start: 54 outliers final: 40 residues processed: 320 average time/residue: 0.3147 time to fit residues: 142.8199 Evaluate side-chains 324 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 282 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 323 GLN Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.6708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16476 Z= 0.214 Angle : 0.745 11.532 22224 Z= 0.384 Chirality : 0.041 0.222 2428 Planarity : 0.004 0.046 2804 Dihedral : 8.978 160.533 2216 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.42 % Allowed : 20.45 % Favored : 77.13 % 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: 0.05 (0.19), residues: 1956 helix: 0.45 (0.13), residues: 1552 sheet: None (None), residues: 0 loop : -1.25 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 344 HIS 0.005 0.001 HIS A 575 PHE 0.025 0.002 PHE D 297 TYR 0.017 0.002 TYR B 118 ARG 0.007 0.001 ARG B 210 *********************** 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 346 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 305 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.6957 (pt0) cc_final: 0.6435 (pp20) REVERT: F 126 ILE cc_start: 0.6862 (mm) cc_final: 0.6580 (mm) REVERT: B 145 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8829 (pt) REVERT: C 13 PHE cc_start: 0.2080 (m-10) cc_final: 0.1689 (m-10) REVERT: C 125 MET cc_start: 0.5817 (tmm) cc_final: 0.5295 (ppp) REVERT: C 146 MET cc_start: 0.3646 (mmm) cc_final: 0.2896 (mmm) REVERT: D 130 GLU cc_start: 0.6818 (pt0) cc_final: 0.6222 (pp20) REVERT: D 145 ILE cc_start: 0.8896 (tp) cc_final: 0.8609 (pt) REVERT: E 76 LYS cc_start: 0.5474 (tptt) cc_final: 0.5033 (tmtt) REVERT: E 125 MET cc_start: 0.5164 (tmm) cc_final: 0.4390 (ptm) REVERT: E 126 ILE cc_start: 0.6991 (mm) cc_final: 0.5994 (mm) REVERT: G 96 HIS cc_start: 0.6781 (m-70) cc_final: 0.6541 (m-70) REVERT: G 130 GLU cc_start: 0.6777 (pt0) cc_final: 0.6266 (pp20) REVERT: G 145 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8703 (pt) REVERT: H 73 MET cc_start: 0.5930 (mmm) cc_final: 0.5574 (mmm) REVERT: H 125 MET cc_start: 0.5213 (tmm) cc_final: 0.4640 (ppp) REVERT: H 126 ILE cc_start: 0.7057 (mm) cc_final: 0.6230 (mm) outliers start: 41 outliers final: 31 residues processed: 325 average time/residue: 0.3215 time to fit residues: 147.8763 Evaluate side-chains 315 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 282 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.6924 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= 0.229 Angle : 0.773 11.566 22224 Z= 0.398 Chirality : 0.042 0.212 2428 Planarity : 0.004 0.043 2804 Dihedral : 8.971 160.926 2216 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.19 % Allowed : 21.16 % Favored : 76.65 % 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: 0.11 (0.19), residues: 1956 helix: 0.50 (0.13), residues: 1536 sheet: None (None), residues: 0 loop : -1.20 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 344 HIS 0.016 0.001 HIS A 96 PHE 0.025 0.002 PHE D 297 TYR 0.019 0.002 TYR B 237 ARG 0.009 0.001 ARG G 325 *********************** 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 330 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 1.853 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: A 130 GLU cc_start: 0.6905 (pt0) cc_final: 0.6371 (pp20) REVERT: F 73 MET cc_start: 0.5733 (mmm) cc_final: 0.5490 (mmm) REVERT: F 126 ILE cc_start: 0.6914 (mm) cc_final: 0.6674 (mm) REVERT: B 145 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8774 (pt) REVERT: C 110 MET cc_start: 0.6231 (ppp) cc_final: 0.5897 (ppp) REVERT: C 125 MET cc_start: 0.5913 (tmm) cc_final: 0.5410 (ppp) REVERT: D 96 HIS cc_start: 0.6777 (m-70) cc_final: 0.6556 (m-70) REVERT: D 130 GLU cc_start: 0.6820 (pt0) cc_final: 0.6180 (pp20) REVERT: D 145 ILE cc_start: 0.8896 (tp) cc_final: 0.8623 (pt) REVERT: D 146 TRP cc_start: 0.6922 (t-100) cc_final: 0.6676 (t60) REVERT: E 76 LYS cc_start: 0.5352 (tptt) cc_final: 0.5060 (tmtt) REVERT: E 125 MET cc_start: 0.5178 (tmm) cc_final: 0.4645 (ptm) REVERT: E 126 ILE cc_start: 0.6966 (mm) cc_final: 0.6230 (mm) REVERT: G 96 HIS cc_start: 0.6806 (m-70) cc_final: 0.6585 (m-70) REVERT: G 145 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8698 (pt) REVERT: H 73 MET cc_start: 0.6082 (mmm) cc_final: 0.5687 (mmm) REVERT: H 125 MET cc_start: 0.5209 (tmm) cc_final: 0.4626 (ppp) REVERT: H 126 ILE cc_start: 0.6977 (mm) cc_final: 0.6229 (mm) outliers start: 37 outliers final: 29 residues processed: 314 average time/residue: 0.3440 time to fit residues: 152.9326 Evaluate side-chains 318 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 100 PHE Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 106 CYS Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain D residue 592 ILE Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.0010 chunk 186 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16476 Z= 0.219 Angle : 0.805 13.974 22224 Z= 0.413 Chirality : 0.043 0.285 2428 Planarity : 0.004 0.042 2804 Dihedral : 9.017 162.282 2216 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.89 % Allowed : 21.87 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.18 (0.19), residues: 1956 helix: 0.57 (0.13), residues: 1532 sheet: None (None), residues: 0 loop : -1.26 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 344 HIS 0.016 0.001 HIS A 96 PHE 0.053 0.002 PHE A 548 TYR 0.020 0.002 TYR B 237 ARG 0.013 0.001 ARG A 547 ********************** 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 337 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 2.048 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: A 130 GLU cc_start: 0.7119 (pt0) cc_final: 0.6592 (pp20) REVERT: F 72 MET cc_start: 0.3505 (pmm) cc_final: 0.3291 (pmm) REVERT: F 126 ILE cc_start: 0.6861 (mm) cc_final: 0.6639 (mm) REVERT: B 145 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8744 (pt) REVERT: C 73 MET cc_start: 0.5967 (mmm) cc_final: 0.5479 (mmm) REVERT: C 125 MET cc_start: 0.5983 (tmm) cc_final: 0.5550 (ppp) REVERT: C 142 PHE cc_start: 0.2749 (t80) cc_final: 0.2109 (t80) REVERT: C 146 MET cc_start: 0.2985 (mmm) cc_final: 0.2339 (mmm) REVERT: D 130 GLU cc_start: 0.6786 (pt0) cc_final: 0.6192 (pp20) REVERT: D 145 ILE cc_start: 0.8922 (tp) cc_final: 0.8630 (pt) REVERT: D 146 TRP cc_start: 0.6805 (t-100) cc_final: 0.6587 (t60) REVERT: E 76 LYS cc_start: 0.5251 (tptt) cc_final: 0.5011 (tmtt) REVERT: E 125 MET cc_start: 0.5156 (tmm) cc_final: 0.4558 (ptm) REVERT: E 126 ILE cc_start: 0.6971 (mm) cc_final: 0.6075 (mm) REVERT: E 127 ARG cc_start: 0.6887 (tpt90) cc_final: 0.6318 (mmm160) REVERT: G 127 TYR cc_start: 0.5478 (t80) cc_final: 0.5078 (t80) REVERT: G 130 GLU cc_start: 0.6720 (pt0) cc_final: 0.6199 (pp20) REVERT: H 125 MET cc_start: 0.5318 (tmm) cc_final: 0.4732 (ppp) REVERT: H 126 ILE cc_start: 0.6792 (mm) cc_final: 0.6057 (mm) outliers start: 32 outliers final: 25 residues processed: 323 average time/residue: 0.3184 time to fit residues: 146.4011 Evaluate side-chains 319 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 HIS Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 324 HIS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain G residue 100 PHE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain G residue 324 HIS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 90 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 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 = 0.4790 r_free = 0.4790 target = 0.182895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.144005 restraints weight = 44594.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.141641 restraints weight = 26053.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.143970 restraints weight = 19866.099| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16476 Z= 0.226 Angle : 0.827 17.147 22224 Z= 0.423 Chirality : 0.044 0.274 2428 Planarity : 0.004 0.042 2804 Dihedral : 9.042 162.725 2216 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.83 % Allowed : 21.93 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.25 (0.19), residues: 1956 helix: 0.63 (0.13), residues: 1528 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 344 HIS 0.015 0.002 HIS A 96 PHE 0.046 0.002 PHE A 548 TYR 0.020 0.002 TYR B 237 ARG 0.012 0.001 ARG G 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.84 seconds wall clock time: 64 minutes 3.24 seconds (3843.24 seconds total)