Starting phenix.real_space_refine (version: dev) on Tue Apr 5 17:09:45 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/04_2022/5k12_8194.pdb" } resolution = 1.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 211": "NH1" <-> "NH2" Residue "E ARG 396": "NH1" <-> "NH2" Residue "E TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F ARG 396": "NH1" <-> "NH2" Residue "F TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 14856 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "D" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "E" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "F" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 10, 'TRANS': 282, 'PCIS': 1} Chain breaks: 1 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "D" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Time building chain proxies: 8.80, per 1000 atoms: 0.59 Number of scatterers: 14856 At special positions: 0 Unit cell: (91.091, 96.187, 159.887, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3660 8.00 N 2454 7.00 C 8670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.81 Conformation dependent library (CDL) restraints added in 2.5 seconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 57.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'A' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 444 through 469 removed outlier: 3.792A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'C' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.570A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 489 Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 418 removed outlier: 3.534A pdb=" N GLU D 415 " --> pdb=" O MET D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 Processing helix chain 'D' and resid 444 through 469 removed outlier: 3.792A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 489 Processing helix chain 'E' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 225 Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU E 415 " --> pdb=" O MET E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 441 Processing helix chain 'E' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 489 Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 225 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 418 removed outlier: 3.534A pdb=" N GLU F 415 " --> pdb=" O MET F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 Processing helix chain 'F' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU A 76 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 76 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU B 76 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU D 76 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU C 76 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU F 76 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2412 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: 4.35 Time building geometry restraints manager: 8.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4323 1.33 - 1.45: 2468 1.45 - 1.57: 7159 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 14070 Sorted by residual: bond pdb=" C LYS E 201 " pdb=" N PRO E 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" C LYS D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.28e+01 bond pdb=" C LYS C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.28e+01 bond pdb=" C LYS A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.329 1.389 -0.059 1.25e-02 6.40e+03 2.26e+01 bond pdb=" C LYS F 201 " pdb=" N PRO F 202 " ideal model delta sigma weight residual 1.329 1.389 -0.059 1.25e-02 6.40e+03 2.24e+01 ... (remaining 14065 not shown) Histogram of bond angle deviations from ideal: 99.69 - 107.54: 600 107.54 - 115.39: 8284 115.39 - 123.24: 9482 123.24 - 131.09: 563 131.09 - 138.94: 67 Bond angle restraints: 18996 Sorted by residual: angle pdb=" C LYS B 201 " pdb=" N PRO B 202 " pdb=" CA PRO B 202 " ideal model delta sigma weight residual 120.14 114.09 6.05 1.06e+00 8.90e-01 3.25e+01 angle pdb=" C LYS A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta sigma weight residual 120.14 114.11 6.03 1.06e+00 8.90e-01 3.23e+01 angle pdb=" C LYS E 201 " pdb=" N PRO E 202 " pdb=" CA PRO E 202 " ideal model delta sigma weight residual 120.14 114.11 6.03 1.06e+00 8.90e-01 3.23e+01 angle pdb=" C LYS D 201 " pdb=" N PRO D 202 " pdb=" CA PRO D 202 " ideal model delta sigma weight residual 120.14 114.13 6.01 1.06e+00 8.90e-01 3.21e+01 angle pdb=" C LYS F 201 " pdb=" N PRO F 202 " pdb=" CA PRO F 202 " ideal model delta sigma weight residual 120.14 114.14 6.00 1.06e+00 8.90e-01 3.21e+01 ... (remaining 18991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.69: 7476 11.69 - 23.38: 678 23.38 - 35.06: 138 35.06 - 46.75: 60 46.75 - 58.44: 12 Dihedral angle restraints: 8364 sinusoidal: 3336 harmonic: 5028 Sorted by residual: dihedral pdb=" CA LYS B 423 " pdb=" C LYS B 423 " pdb=" N HIS B 424 " pdb=" CA HIS B 424 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS C 423 " pdb=" C LYS C 423 " pdb=" N HIS C 424 " pdb=" CA HIS C 424 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS E 423 " pdb=" C LYS E 423 " pdb=" N HIS E 424 " pdb=" CA HIS E 424 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1460 0.058 - 0.116: 442 0.116 - 0.174: 128 0.174 - 0.233: 10 0.233 - 0.291: 12 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CG LEU B 397 " pdb=" CB LEU B 397 " pdb=" CD1 LEU B 397 " pdb=" CD2 LEU B 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CG LEU F 397 " pdb=" CB LEU F 397 " pdb=" CD1 LEU F 397 " pdb=" CD2 LEU F 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU E 397 " pdb=" CB LEU E 397 " pdb=" CD1 LEU E 397 " pdb=" CD2 LEU E 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 2049 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 436 " 0.023 2.00e-02 2.50e+03 2.14e-02 7.99e+00 pdb=" CG PHE D 436 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 436 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 436 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 436 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 436 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 436 " -0.023 2.00e-02 2.50e+03 2.13e-02 7.92e+00 pdb=" CG PHE C 436 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 436 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 436 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 436 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 436 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 436 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 436 " 0.023 2.00e-02 2.50e+03 2.13e-02 7.90e+00 pdb=" CG PHE F 436 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE F 436 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 436 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 436 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 436 " 0.008 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 672 2.62 - 3.19: 14245 3.19 - 3.76: 25473 3.76 - 4.33: 38298 4.33 - 4.90: 57865 Nonbonded interactions: 136553 Sorted by model distance: nonbonded pdb=" O ARG F 211 " pdb=" O HOH F 601 " model vdw 2.051 2.440 nonbonded pdb=" O ARG B 211 " pdb=" O HOH B 601 " model vdw 2.051 2.440 nonbonded pdb=" O ARG A 211 " pdb=" O HOH A 601 " model vdw 2.051 2.440 nonbonded pdb=" O ARG D 211 " pdb=" O HOH D 601 " model vdw 2.051 2.440 nonbonded pdb=" O ARG E 211 " pdb=" O HOH E 601 " model vdw 2.051 2.440 ... (remaining 136548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8670 2.51 5 N 2454 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 4.500 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 42.760 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 0.060 14070 Z= 0.557 Angle : 0.975 13.941 18996 Z= 0.546 Chirality : 0.061 0.291 2052 Planarity : 0.007 0.046 2454 Dihedral : 10.269 58.440 5172 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 1740 helix: -2.23 (0.13), residues: 924 sheet: -0.80 (0.25), residues: 288 loop : -0.57 (0.27), residues: 528 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 373 time to evaluate : 1.874 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 375 average time/residue: 1.3511 time to fit residues: 553.2144 Evaluate side-chains 187 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 388 ASN A 463 GLN A 484 ASN ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 437 GLN B 463 GLN B 484 ASN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 374 ASN C 388 ASN C 484 ASN ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN D 484 ASN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN E 484 ASN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 484 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 14070 Z= 0.228 Angle : 0.635 8.091 18996 Z= 0.334 Chirality : 0.044 0.153 2052 Planarity : 0.006 0.059 2454 Dihedral : 4.929 21.443 1944 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.19), residues: 1740 helix: 0.56 (0.16), residues: 918 sheet: -0.61 (0.27), residues: 282 loop : -0.19 (0.27), residues: 540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 1.751 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 226 average time/residue: 1.2831 time to fit residues: 319.2598 Evaluate side-chains 163 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 209 HIS A 374 ASN ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 189 HIS B 209 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 209 HIS C 388 ASN D 82 HIS D 84 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 209 HIS D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS E 209 HIS ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 HIS F 437 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.032 14070 Z= 0.362 Angle : 0.612 5.423 18996 Z= 0.322 Chirality : 0.046 0.130 2052 Planarity : 0.005 0.057 2454 Dihedral : 4.718 18.006 1944 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.20), residues: 1740 helix: 1.44 (0.16), residues: 936 sheet: -0.71 (0.28), residues: 288 loop : 0.26 (0.28), residues: 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 1.743 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 161 average time/residue: 1.5164 time to fit residues: 265.6900 Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.1122 time to fit residues: 4.7450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.0870 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN B 57 HIS B 84 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS F 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14070 Z= 0.204 Angle : 0.520 11.230 18996 Z= 0.275 Chirality : 0.042 0.152 2052 Planarity : 0.005 0.068 2454 Dihedral : 4.294 18.965 1944 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1740 helix: 2.09 (0.16), residues: 936 sheet: -0.60 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.770 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 174 average time/residue: 1.5580 time to fit residues: 294.9040 Evaluate side-chains 142 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.962 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 3.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 HIS ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 85 HIS F 437 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.791 Angle : 1.087 106.092 18996 Z= 0.478 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 1.745 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 1.5805 time to fit residues: 253.0648 Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 2.2848 time to fit residues: 4.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 41 optimal weight: 0.9990 chunk 168 optimal weight: 50.0000 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 137 time to evaluate : 1.819 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 140 average time/residue: 1.5032 time to fit residues: 229.5560 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.3665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.788 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 139 average time/residue: 1.5267 time to fit residues: 231.4121 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.767 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.4648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.816 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 139 average time/residue: 1.5085 time to fit residues: 228.9536 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.4993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.756 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 139 average time/residue: 1.5337 time to fit residues: 232.2857 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.3521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.802 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 139 average time/residue: 1.4854 time to fit residues: 225.4798 Evaluate side-chains 139 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.4491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.098256 restraints weight = 24235.029| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.44 r_work: 0.3719 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 1.29 restraints_weight: 0.2500 r_work: 0.3704 rms_B_bonded: 1.31 restraints_weight: 0.1250 r_work: 0.3696 rms_B_bonded: 1.36 restraints_weight: 0.0625 r_work: 0.3688 rms_B_bonded: 1.44 restraints_weight: 0.0312 r_work: 0.3678 rms_B_bonded: 1.55 restraints_weight: 0.0156 r_work: 0.3668 rms_B_bonded: 1.68 restraints_weight: 0.0078 r_work: 0.3657 rms_B_bonded: 1.84 restraints_weight: 0.0039 r_work: 0.3645 rms_B_bonded: 2.02 restraints_weight: 0.0020 r_work: 0.3631 rms_B_bonded: 2.24 restraints_weight: 0.0010 r_work: 0.3617 rms_B_bonded: 2.49 restraints_weight: 0.0005 r_work: 0.3601 rms_B_bonded: 2.78 restraints_weight: 0.0002 r_work: 0.3583 rms_B_bonded: 3.11 restraints_weight: 0.0001 r_work: 0.3564 rms_B_bonded: 3.49 restraints_weight: 0.0001 r_work: 0.3544 rms_B_bonded: 3.92 restraints_weight: 0.0000 r_work: 0.3523 rms_B_bonded: 4.41 restraints_weight: 0.0000 r_work: 0.3500 rms_B_bonded: 4.98 restraints_weight: 0.0000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.859 14070 Z= 0.795 Angle : 1.103 106.100 18996 Z= 0.485 Chirality : 0.044 0.394 2052 Planarity : 0.005 0.070 2454 Dihedral : 4.267 17.631 1944 Min Nonbonded Distance : 1.444 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.20), residues: 1740 helix: 2.13 (0.17), residues: 936 sheet: -0.59 (0.29), residues: 282 loop : 0.46 (0.29), residues: 522 =============================================================================== Job complete usr+sys time: 5181.20 seconds wall clock time: 93 minutes 49.96 seconds (5629.96 seconds total)