Starting phenix.real_space_refine on Sat Mar 16 13:50:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/03_2024/5k12_8194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/03_2024/5k12_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_8194/03_2024/5k12_8194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/03_2024/5k12_8194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/03_2024/5k12_8194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/03_2024/5k12_8194.pdb" } resolution = 1.8 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= 0.003 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 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. 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-5265/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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} 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: 8.96, per 1000 atoms: 0.60 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: 6.33 Conformation dependent library (CDL) restraints added in 2.3 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: 1.36 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: 4.02 Time building geometry restraints manager: 6.71 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 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.220 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 40.160 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 % Allowed : 0.82 % Favored : 98.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.005 TRP D 178 HIS 0.011 0.004 HIS E 82 PHE 0.049 0.006 PHE D 436 TYR 0.043 0.005 TYR D 95 ARG 0.009 0.001 ARG D 478 *********************** 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 : 1.755 Fit side-chains revert: symmetry clash REVERT: B 101 VAL cc_start: 0.8395 (t) cc_final: 0.8158 (p) REVERT: B 486 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6388 (mt) REVERT: C 101 VAL cc_start: 0.8253 (t) cc_final: 0.8034 (p) REVERT: D 486 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6469 (mt) REVERT: E 486 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6495 (mt) REVERT: F 486 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6427 (mt) outliers start: 12 outliers final: 0 residues processed: 375 average time/residue: 1.4361 time to fit residues: 585.3357 Evaluate side-chains 189 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain F residue 486 ILE 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: 0.0570 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6983 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14070 Z= 0.184 Angle : 0.597 6.969 18996 Z= 0.315 Chirality : 0.044 0.152 2052 Planarity : 0.006 0.057 2454 Dihedral : 4.937 22.137 1952 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.23 % Allowed : 10.38 % Favored : 88.39 % 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: 0.10 (0.19), residues: 1740 helix: 0.60 (0.16), residues: 918 sheet: -0.58 (0.28), residues: 282 loop : -0.22 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 385 HIS 0.003 0.001 HIS B 57 PHE 0.016 0.002 PHE A 436 TYR 0.010 0.001 TYR E 95 ARG 0.009 0.001 ARG A 466 *********************** 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 230 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 212 time to evaluate : 1.634 Fit side-chains REVERT: A 176 MET cc_start: 0.7750 (mmp) cc_final: 0.7463 (mmt) outliers start: 18 outliers final: 0 residues processed: 223 average time/residue: 1.3320 time to fit residues: 325.7462 Evaluate side-chains 164 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 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** D 463 GLN E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS E 209 HIS E 437 GLN 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 ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14070 Z= 0.400 Angle : 0.616 5.485 18996 Z= 0.328 Chirality : 0.047 0.136 2052 Planarity : 0.006 0.059 2454 Dihedral : 4.766 17.951 1944 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.30 % Allowed : 11.95 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1740 helix: 1.40 (0.16), residues: 936 sheet: -0.73 (0.28), residues: 288 loop : 0.25 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 385 HIS 0.005 0.002 HIS E 391 PHE 0.023 0.002 PHE B 436 TYR 0.018 0.002 TYR B 382 ARG 0.007 0.001 ARG C 419 *********************** 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 180 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.783 Fit side-chains REVERT: B 140 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6634 (mt-10) outliers start: 19 outliers final: 6 residues processed: 171 average time/residue: 1.6731 time to fit residues: 309.7959 Evaluate side-chains 150 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 205 GLN ** 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 ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS ** F 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14070 Z= 0.256 Angle : 0.517 5.328 18996 Z= 0.275 Chirality : 0.043 0.127 2052 Planarity : 0.005 0.064 2454 Dihedral : 4.417 18.999 1944 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.02 % Allowed : 12.43 % Favored : 86.54 % 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: 1.55 (0.20), residues: 1740 helix: 1.98 (0.17), residues: 936 sheet: -0.66 (0.28), residues: 288 loop : 0.44 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 385 HIS 0.004 0.001 HIS C 450 PHE 0.014 0.002 PHE A 436 TYR 0.012 0.001 TYR F 382 ARG 0.004 0.000 ARG F 466 *********************** 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: 15 poor density : 163 time to evaluate : 1.792 Fit side-chains REVERT: B 134 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8087 (mmmm) REVERT: B 140 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: C 374 ASN cc_start: 0.7515 (m110) cc_final: 0.7069 (t0) REVERT: D 134 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8079 (mmmm) REVERT: E 374 ASN cc_start: 0.7632 (m110) cc_final: 0.7143 (t0) REVERT: F 374 ASN cc_start: 0.7656 (m110) cc_final: 0.7329 (t0) outliers start: 15 outliers final: 4 residues processed: 173 average time/residue: 1.6341 time to fit residues: 305.7537 Evaluate side-chains 146 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 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 414 GLN D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14070 Z= 0.344 Angle : 0.549 6.018 18996 Z= 0.291 Chirality : 0.045 0.126 2052 Planarity : 0.005 0.062 2454 Dihedral : 4.444 17.419 1944 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.43 % Allowed : 12.98 % Favored : 85.59 % 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: 1.64 (0.20), residues: 1740 helix: 2.09 (0.17), residues: 936 sheet: -0.73 (0.28), residues: 288 loop : 0.49 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 385 HIS 0.005 0.002 HIS C 82 PHE 0.017 0.002 PHE C 436 TYR 0.014 0.002 TYR B 382 ARG 0.003 0.000 ARG F 466 *********************** 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 173 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.925 Fit side-chains REVERT: B 140 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6564 (mt-10) REVERT: D 134 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8150 (mmmm) REVERT: F 374 ASN cc_start: 0.7701 (m110) cc_final: 0.7353 (t0) outliers start: 21 outliers final: 5 residues processed: 170 average time/residue: 1.5603 time to fit residues: 287.6506 Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.0870 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 168 optimal weight: 0.2980 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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 205 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 205 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** F 57 HIS ** 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: 0.7044 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14070 Z= 0.142 Angle : 0.449 6.713 18996 Z= 0.239 Chirality : 0.040 0.125 2052 Planarity : 0.005 0.061 2454 Dihedral : 4.051 21.252 1944 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.89 % Allowed : 13.39 % Favored : 85.72 % 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: 2.10 (0.21), residues: 1740 helix: 2.49 (0.17), residues: 936 sheet: -0.59 (0.30), residues: 282 loop : 0.66 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS C 450 PHE 0.010 0.001 PHE A 436 TYR 0.011 0.001 TYR F 471 ARG 0.003 0.000 ARG C 66 *********************** 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 183 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.755 Fit side-chains REVERT: B 140 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6487 (mt-10) REVERT: C 374 ASN cc_start: 0.7478 (m110) cc_final: 0.7058 (t0) REVERT: D 134 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8039 (mmmm) REVERT: E 374 ASN cc_start: 0.7548 (m110) cc_final: 0.7096 (t0) outliers start: 13 outliers final: 4 residues processed: 183 average time/residue: 1.5296 time to fit residues: 304.3351 Evaluate side-chains 151 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain D residue 134 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 374 ASN B 437 GLN ** 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 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 437 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14070 Z= 0.317 Angle : 0.518 6.168 18996 Z= 0.277 Chirality : 0.044 0.124 2052 Planarity : 0.005 0.059 2454 Dihedral : 4.247 19.522 1944 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.37 % Allowed : 13.87 % Favored : 84.77 % 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: 2.04 (0.21), residues: 1740 helix: 2.41 (0.17), residues: 936 sheet: -0.62 (0.29), residues: 282 loop : 0.69 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 PHE 0.024 0.002 PHE C 220 TYR 0.015 0.001 TYR D 78 ARG 0.011 0.000 ARG E 419 *********************** 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 169 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.945 Fit side-chains REVERT: B 134 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (mmmm) REVERT: C 374 ASN cc_start: 0.7532 (m110) cc_final: 0.7082 (t0) REVERT: D 134 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8126 (mmmm) REVERT: E 374 ASN cc_start: 0.7644 (m110) cc_final: 0.7143 (t0) outliers start: 20 outliers final: 4 residues processed: 166 average time/residue: 1.4736 time to fit residues: 266.5044 Evaluate side-chains 145 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 134 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 205 GLN B 374 ASN B 437 GLN ** 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 205 GLN D 374 ASN D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 437 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14070 Z= 0.277 Angle : 0.512 6.512 18996 Z= 0.274 Chirality : 0.043 0.155 2052 Planarity : 0.005 0.059 2454 Dihedral : 4.253 20.154 1944 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.09 % Allowed : 14.28 % Favored : 84.63 % 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: 2.02 (0.21), residues: 1740 helix: 2.39 (0.17), residues: 936 sheet: -0.65 (0.29), residues: 282 loop : 0.71 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 PHE 0.013 0.002 PHE A 436 TYR 0.013 0.001 TYR C 113 ARG 0.017 0.000 ARG F 419 *********************** 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 168 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.601 Fit side-chains REVERT: B 134 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8086 (mmmm) REVERT: C 374 ASN cc_start: 0.7518 (m110) cc_final: 0.7074 (t0) REVERT: E 169 MET cc_start: 0.7313 (pmt) cc_final: 0.7075 (mmm) REVERT: E 374 ASN cc_start: 0.7643 (m110) cc_final: 0.7156 (t0) REVERT: F 169 MET cc_start: 0.7314 (pmt) cc_final: 0.7071 (mmm) outliers start: 16 outliers final: 5 residues processed: 167 average time/residue: 1.3794 time to fit residues: 250.8426 Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.8980 chunk 160 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 193 ASN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 463 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 437 GLN E 463 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 437 GLN F 463 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14070 Z= 0.221 Angle : 0.489 7.785 18996 Z= 0.263 Chirality : 0.042 0.147 2052 Planarity : 0.005 0.062 2454 Dihedral : 4.168 20.389 1944 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.55 % Allowed : 15.03 % Favored : 84.43 % 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: 2.09 (0.21), residues: 1740 helix: 2.45 (0.17), residues: 936 sheet: -0.61 (0.29), residues: 282 loop : 0.73 (0.30), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 PHE 0.026 0.001 PHE C 220 TYR 0.012 0.001 TYR C 113 ARG 0.010 0.000 ARG C 419 *********************** 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 162 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.883 Fit side-chains REVERT: B 134 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8059 (mmmm) REVERT: C 374 ASN cc_start: 0.7503 (m110) cc_final: 0.7067 (t0) REVERT: E 169 MET cc_start: 0.7307 (pmt) cc_final: 0.7055 (mmm) REVERT: E 374 ASN cc_start: 0.7625 (m110) cc_final: 0.7153 (t0) REVERT: F 169 MET cc_start: 0.7314 (pmt) cc_final: 0.7050 (mmm) outliers start: 8 outliers final: 4 residues processed: 161 average time/residue: 1.5298 time to fit residues: 268.2243 Evaluate side-chains 144 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 139 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 173 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 205 GLN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 205 GLN ** D 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN E 437 GLN E 463 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 437 GLN F 463 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14070 Z= 0.364 Angle : 0.566 6.250 18996 Z= 0.306 Chirality : 0.045 0.145 2052 Planarity : 0.006 0.086 2454 Dihedral : 4.392 20.096 1944 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 15.44 % Favored : 83.95 % 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: 1.86 (0.21), residues: 1740 helix: 2.25 (0.17), residues: 936 sheet: -0.68 (0.29), residues: 282 loop : 0.62 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.002 HIS F 450 PHE 0.016 0.002 PHE C 436 TYR 0.013 0.002 TYR B 382 ARG 0.021 0.001 ARG F 419 ********************** 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 153 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.846 Fit side-chains REVERT: B 134 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8131 (mmmm) REVERT: E 169 MET cc_start: 0.7402 (pmt) cc_final: 0.7132 (mmm) REVERT: F 169 MET cc_start: 0.7408 (pmt) cc_final: 0.7132 (mmm) outliers start: 9 outliers final: 4 residues processed: 153 average time/residue: 1.5368 time to fit residues: 255.7154 Evaluate side-chains 142 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 475 LEU 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: 0.5980 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 374 ASN B 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN D 463 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN E 463 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 437 GLN F 463 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.107410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.095401 restraints weight = 24498.342| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.42 r_work: 0.3619 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14070 Z= 0.261 Angle : 0.510 6.037 18996 Z= 0.277 Chirality : 0.043 0.146 2052 Planarity : 0.005 0.063 2454 Dihedral : 4.247 20.651 1944 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.68 % Allowed : 15.16 % Favored : 84.15 % 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: 1.95 (0.21), residues: 1740 helix: 2.34 (0.17), residues: 936 sheet: -0.66 (0.29), residues: 282 loop : 0.66 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 PHE 0.013 0.001 PHE C 436 TYR 0.013 0.001 TYR C 113 ARG 0.013 0.001 ARG F 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.71 seconds wall clock time: 115 minutes 49.99 seconds (6949.99 seconds total)