Starting phenix.real_space_refine on Sat Sep 28 03:01:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/09_2024/7uaf_26423.cif" } resolution = 2.4 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= 0.002 sd= 0.036 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 4 6.06 5 S 84 5.16 5 C 11246 2.51 5 N 2979 2.21 5 O 3543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17864 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 4319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4319 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Chain: "A" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4313 Classifications: {'peptide': 535} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 515} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4295 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 512} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4257 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, ' ZN': 1, 'M6X': 1, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.98, per 1000 atoms: 0.61 Number of scatterers: 17864 At special positions: 0 Unit cell: (110.24, 168.54, 135.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 8 19.99 S 84 16.00 O 3543 8.00 N 2979 7.00 C 11246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 147 " distance=1.99 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS A 308 " distance=2.05 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 431 " distance=2.06 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS B 559 " distance=2.04 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 259 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.01 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.06 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 259 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 277 " distance=2.04 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 431 " distance=2.05 Simple disulfide: pdb=" SG CYS C 557 " - pdb=" SG CYS C 559 " distance=2.05 Simple disulfide: pdb=" SG CYS D 107 " - pdb=" SG CYS D 259 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=2.01 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 277 " distance=2.04 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.06 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " BETA1-6 " NAG H 1 " - " FUC H 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " " NAG R 1 " - " FUC R 4 " NAG-ASN " NAG A 705 " - " ASN A 440 " " NAG B 705 " - " ASN B 440 " " NAG C 705 " - " ASN C 440 " " NAG D 705 " - " ASN D 440 " " NAG E 1 " - " ASN B 140 " " NAG F 1 " - " ASN B 258 " " NAG G 1 " - " ASN B 222 " " NAG H 1 " - " ASN B 414 " " NAG I 1 " - " ASN A 258 " " NAG J 1 " - " ASN A 222 " " NAG K 1 " - " ASN A 414 " " NAG L 1 " - " ASN A 140 " " NAG M 1 " - " ASN C 140 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 414 " " NAG P 1 " - " ASN D 140 " " NAG Q 1 " - " ASN D 222 " " NAG R 1 " - " ASN D 414 " Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 155 " pdb="ZN ZN A 703 " - pdb=" NE2 HIS A 159 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 165 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 155 " pdb="ZN ZN B 703 " - pdb=" NE2 HIS B 159 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 165 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 155 " pdb="ZN ZN C 703 " - pdb=" NE2 HIS C 159 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 155 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 159 " 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3976 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 39 sheets defined 22.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 149 through 162 Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 171 through 174 Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 232 through 238 Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 440 through 448 removed outlier: 3.505A pdb=" N GLU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 546 through 551 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 171 through 174 Processing helix chain 'A' and resid 180 through 183 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 411 through 415 removed outlier: 3.506A pdb=" N SER A 415 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 516 through 520 Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.901A pdb=" N ARG C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 106 Processing helix chain 'C' and resid 149 through 161 Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 171 through 174 Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.651A pdb=" N ILE C 183 " --> pdb=" O TRP C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 232 through 238 removed outlier: 3.627A pdb=" N PHE C 235 " --> pdb=" O ILE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 440 through 448 removed outlier: 4.146A pdb=" N GLU C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 497 Processing helix chain 'C' and resid 516 through 520 Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 573 through 577 removed outlier: 3.679A pdb=" N LYS C 577 " --> pdb=" O HIS C 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 573 through 577' Processing helix chain 'C' and resid 597 through 600 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.527A pdb=" N ARG D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 180 through 183 Processing helix chain 'D' and resid 186 through 192 removed outlier: 4.589A pdb=" N HIS D 189 " --> pdb=" O GLY D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 440 through 448 removed outlier: 4.031A pdb=" N GLU D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 Processing helix chain 'D' and resid 535 through 539 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.930A pdb=" N PHE B 122 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 82 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AA4, first strand: chain 'B' and resid 265 through 269 Processing sheet with id=AA5, first strand: chain 'B' and resid 265 through 269 removed outlier: 5.801A pdb=" N LEU B 421 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS B 349 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP B 423 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE B 347 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 280 through 281 removed outlier: 6.812A pdb=" N LEU B 358 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR B 379 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 360 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 434 through 438 Processing sheet with id=AA8, first strand: chain 'B' and resid 454 through 455 Processing sheet with id=AA9, first strand: chain 'B' and resid 454 through 455 removed outlier: 3.951A pdb=" N GLY B 466 " --> pdb=" O CYS B 489 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 482 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 569 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 552 through 553 Processing sheet with id=AB2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'A' and resid 110 through 112 removed outlier: 7.940A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AB5, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AB6, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.750A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 280 through 281 removed outlier: 6.777A pdb=" N LEU A 358 " --> pdb=" O THR A 379 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A 379 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A 360 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AB9, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AC1, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.983A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 482 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 569 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 552 through 553 Processing sheet with id=AC3, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.082A pdb=" N ILE C 79 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE C 122 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 82 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AC6, first strand: chain 'C' and resid 265 through 269 Processing sheet with id=AC7, first strand: chain 'C' and resid 265 through 269 removed outlier: 5.721A pdb=" N LEU C 421 " --> pdb=" O LYS C 349 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LYS C 349 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASP C 423 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE C 347 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 280 through 281 removed outlier: 6.673A pdb=" N LEU C 358 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR C 379 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 360 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 434 through 438 Processing sheet with id=AD1, first strand: chain 'C' and resid 454 through 455 Processing sheet with id=AD2, first strand: chain 'C' and resid 454 through 455 removed outlier: 3.828A pdb=" N GLY C 466 " --> pdb=" O CYS C 489 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE C 571 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 484 " --> pdb=" O GLY C 569 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY C 569 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N PHE C 486 " --> pdb=" O TRP C 567 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TRP C 567 " --> pdb=" O PHE C 486 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL C 488 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU C 565 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 551 through 553 Processing sheet with id=AD4, first strand: chain 'D' and resid 110 through 112 removed outlier: 8.023A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AD6, first strand: chain 'D' and resid 265 through 269 Processing sheet with id=AD7, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.709A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 280 through 281 removed outlier: 6.853A pdb=" N LEU D 358 " --> pdb=" O THR D 379 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N THR D 379 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 360 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AE1, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AE2, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.863A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 482 " --> pdb=" O GLY D 569 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 551 through 553 624 hydrogen bonds defined for protein. 1440 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: 7.34 Time building geometry restraints manager: 4.99 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: 4866 1.33 - 1.45: 3929 1.45 - 1.58: 9386 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 18301 Sorted by residual: bond pdb=" C VAL A 300 " pdb=" N ASP A 301 " ideal model delta sigma weight residual 1.328 1.246 0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C ASP C 385 " pdb=" N HIS C 386 " ideal model delta sigma weight residual 1.332 1.263 0.070 1.29e-02 6.01e+03 2.93e+01 bond pdb=" C ASP B 385 " pdb=" N HIS B 386 " ideal model delta sigma weight residual 1.332 1.279 0.054 1.29e-02 6.01e+03 1.74e+01 bond pdb=" C VAL D 300 " pdb=" N ASP D 301 " ideal model delta sigma weight residual 1.330 1.387 -0.057 1.38e-02 5.25e+03 1.72e+01 bond pdb=" C ARG B 579 " pdb=" N SER B 580 " ideal model delta sigma weight residual 1.330 1.272 0.058 1.52e-02 4.33e+03 1.47e+01 ... (remaining 18296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 17188 1.76 - 3.53: 6310 3.53 - 5.29: 1177 5.29 - 7.06: 146 7.06 - 8.82: 14 Bond angle restraints: 24835 Sorted by residual: angle pdb=" N ARG D 284 " pdb=" CA ARG D 284 " pdb=" C ARG D 284 " ideal model delta sigma weight residual 112.23 104.24 7.99 1.26e+00 6.30e-01 4.02e+01 angle pdb=" C THR C 433 " pdb=" N GLY C 434 " pdb=" CA GLY C 434 " ideal model delta sigma weight residual 121.65 125.87 -4.22 6.80e-01 2.16e+00 3.85e+01 angle pdb=" CA PHE D 590 " pdb=" CB PHE D 590 " pdb=" CG PHE D 590 " ideal model delta sigma weight residual 113.80 119.58 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" N ASP D 512 " pdb=" CA ASP D 512 " pdb=" C ASP D 512 " ideal model delta sigma weight residual 109.25 100.43 8.82 1.53e+00 4.27e-01 3.32e+01 angle pdb=" CA ASP C 301 " pdb=" CB ASP C 301 " pdb=" CG ASP C 301 " ideal model delta sigma weight residual 112.60 118.12 -5.52 1.00e+00 1.00e+00 3.05e+01 ... (remaining 24830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 10706 21.54 - 43.08: 497 43.08 - 64.63: 84 64.63 - 86.17: 47 86.17 - 107.71: 20 Dihedral angle restraints: 11354 sinusoidal: 5162 harmonic: 6192 Sorted by residual: dihedral pdb=" CB CYS C 128 " pdb=" SG CYS C 128 " pdb=" SG CYS C 147 " pdb=" CB CYS C 147 " ideal model delta sinusoidal sigma weight residual 93.00 150.93 -57.93 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 557 " pdb=" SG CYS D 557 " pdb=" SG CYS D 559 " pdb=" CB CYS D 559 " ideal model delta sinusoidal sigma weight residual -86.00 -143.42 57.42 1 1.00e+01 1.00e-02 4.43e+01 dihedral pdb=" CB CYS C 557 " pdb=" SG CYS C 557 " pdb=" SG CYS C 559 " pdb=" CB CYS C 559 " ideal model delta sinusoidal sigma weight residual -86.00 -142.55 56.55 1 1.00e+01 1.00e-02 4.31e+01 ... (remaining 11351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1667 0.087 - 0.174: 849 0.174 - 0.262: 183 0.262 - 0.349: 42 0.349 - 0.436: 12 Chirality restraints: 2753 Sorted by residual: chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 FUC H 4 " pdb=" O6 NAG H 1 " pdb=" C2 FUC H 4 " pdb=" O5 FUC H 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.07e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 2.88e+01 ... (remaining 2750 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " -0.319 2.00e-02 2.50e+03 2.75e-01 9.49e+02 pdb=" C7 NAG L 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " 0.477 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 705 " -0.320 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG A 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG A 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A 705 " 0.472 2.00e-02 2.50e+03 pdb=" O7 NAG A 705 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 705 " -0.318 2.00e-02 2.50e+03 2.70e-01 9.10e+02 pdb=" C7 NAG B 705 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG B 705 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B 705 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG B 705 " -0.048 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 38 2.41 - 3.03: 9913 3.03 - 3.65: 25430 3.65 - 4.28: 44391 4.28 - 4.90: 70528 Nonbonded interactions: 150300 Sorted by model distance: nonbonded pdb=" O CYS D 128 " pdb=" O6 M6X D 701 " model vdw 1.783 3.040 nonbonded pdb=" OH TYR B 214 " pdb=" O3 M6X B 701 " model vdw 1.855 3.040 nonbonded pdb=" O CYS D 128 " pdb=" N2 M6X D 701 " model vdw 1.856 3.120 nonbonded pdb=" OD1 ASP B 285 " pdb="CA CA B 702 " model vdw 1.861 2.510 nonbonded pdb=" OH TYR A 214 " pdb=" O3 M6X A 701 " model vdw 1.999 3.040 ... (remaining 150295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 600 or resid 701 through 705)) selection = (chain 'B' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 295 or resid 299 through 332 or (res \ id 333 and (name N or name CA or name C or name O or name CB )) or resid 334 thr \ ough 475 or (resid 476 and (name N or name CA or name C or name O or name CB )) \ or resid 477 through 600 or resid 701 through 705)) selection = (chain 'C' and (resid 66 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 169 or resid 172 through 200 or re \ sid 205 through 259 or (resid 260 through 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 475 or (resid 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 600 or resid 701 thr \ ough 705)) selection = (chain 'D' and (resid 66 through 295 or resid 299 through 475 or (resid 476 and \ (name N or name CA or name C or name O or name CB )) or resid 477 through 600 or \ resid 701 through 705)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'O' selection = chain 'R' } 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: 0.540 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 44.880 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.012 0.082 18301 Z= 0.783 Angle : 1.800 8.822 24835 Z= 1.212 Chirality : 0.105 0.436 2753 Planarity : 0.021 0.275 3174 Dihedral : 14.566 107.709 7315 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.16 % Allowed : 3.11 % Favored : 96.73 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 10.53 % 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: -0.18 (0.17), residues: 2117 helix: -1.52 (0.27), residues: 259 sheet: 0.67 (0.21), residues: 515 loop : -0.08 (0.17), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.138 0.022 TRP A 436 HIS 0.024 0.004 HIS C 573 PHE 0.073 0.012 PHE B 593 TYR 0.105 0.018 TYR A 313 ARG 0.010 0.001 ARG D 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 564 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 111 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7864 (pttp) REVERT: B 299 GLU cc_start: 0.6447 (mp0) cc_final: 0.6071 (mp0) REVERT: B 315 MET cc_start: 0.8558 (mmm) cc_final: 0.8351 (mmm) REVERT: B 578 ARG cc_start: 0.7822 (mtt90) cc_final: 0.7566 (mtt180) REVERT: A 286 ASP cc_start: 0.6452 (t70) cc_final: 0.6163 (t0) REVERT: A 350 MET cc_start: 0.8607 (mtp) cc_final: 0.8362 (mtt) REVERT: C 217 PHE cc_start: 0.8436 (m-80) cc_final: 0.8150 (m-80) REVERT: C 251 GLU cc_start: 0.7011 (tt0) cc_final: 0.6687 (tt0) REVERT: C 279 MET cc_start: 0.4682 (mtt) cc_final: 0.4290 (mtt) REVERT: C 313 TYR cc_start: 0.7899 (m-80) cc_final: 0.7514 (m-80) REVERT: C 350 MET cc_start: 0.8794 (mtp) cc_final: 0.8575 (mtm) REVERT: C 370 ASN cc_start: 0.7507 (t0) cc_final: 0.7157 (t0) REVERT: C 422 ASP cc_start: 0.7992 (t0) cc_final: 0.7016 (m-30) REVERT: C 561 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7738 (mtt180) REVERT: D 113 TYR cc_start: 0.8169 (t80) cc_final: 0.7868 (t80) REVERT: D 215 GLN cc_start: 0.7717 (pt0) cc_final: 0.6772 (pt0) REVERT: D 227 THR cc_start: 0.8207 (m) cc_final: 0.7951 (p) REVERT: D 313 TYR cc_start: 0.7851 (m-80) cc_final: 0.7416 (m-80) REVERT: D 422 ASP cc_start: 0.8450 (t0) cc_final: 0.7429 (m-30) REVERT: D 489 CYS cc_start: 0.7588 (m) cc_final: 0.7383 (m) REVERT: D 502 GLU cc_start: 0.6554 (tt0) cc_final: 0.6344 (tt0) REVERT: D 578 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7586 (mtm-85) REVERT: D 579 ARG cc_start: 0.7415 (mtp85) cc_final: 0.6896 (mtt-85) outliers start: 3 outliers final: 0 residues processed: 565 average time/residue: 1.3127 time to fit residues: 825.6215 Evaluate side-chains 469 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 72 ASN B 145 GLN B 215 GLN B 307 GLN B 341 GLN B 413 GLN B 574 GLN A 66 ASN A 72 ASN A 145 GLN A 296 GLN A 447 ASN C 72 ASN C 189 HIS C 341 GLN C 513 GLN C 554 HIS D 72 ASN D 341 GLN D 513 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18301 Z= 0.208 Angle : 0.636 8.657 24835 Z= 0.340 Chirality : 0.046 0.168 2753 Planarity : 0.004 0.029 3174 Dihedral : 8.865 65.908 3286 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.06 % Allowed : 10.61 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.05 (0.17), residues: 2117 helix: -0.16 (0.30), residues: 266 sheet: 0.32 (0.21), residues: 562 loop : 0.04 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 361 HIS 0.010 0.001 HIS B 155 PHE 0.023 0.002 PHE C 245 TYR 0.020 0.001 TYR D 97 ARG 0.007 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 481 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7761 (p0) REVERT: B 574 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6603 (pt0) REVERT: A 66 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 316 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: C 154 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 156 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7038 (mm-30) REVERT: C 217 PHE cc_start: 0.8490 (m-80) cc_final: 0.8182 (m-80) REVERT: C 251 GLU cc_start: 0.6952 (tt0) cc_final: 0.6690 (tt0) REVERT: C 279 MET cc_start: 0.4788 (mtt) cc_final: 0.4537 (mtp) REVERT: C 455 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: D 113 TYR cc_start: 0.8124 (t80) cc_final: 0.7814 (t80) REVERT: D 154 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 207 ASP cc_start: 0.6804 (t0) cc_final: 0.6584 (t0) REVERT: D 313 TYR cc_start: 0.7880 (m-80) cc_final: 0.7649 (m-80) outliers start: 39 outliers final: 15 residues processed: 496 average time/residue: 1.3332 time to fit residues: 734.0435 Evaluate side-chains 473 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 453 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 356 ASP Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 370 ASN B 558 ASN B 574 GLN A 66 ASN A 399 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 291 HIS C 474 ASN D 136 HIS D 292 GLN D 341 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 18301 Z= 0.534 Angle : 0.724 8.564 24835 Z= 0.385 Chirality : 0.052 0.162 2753 Planarity : 0.005 0.064 3174 Dihedral : 7.279 44.216 3286 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.43 % Allowed : 13.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.17), residues: 2117 helix: -0.15 (0.30), residues: 265 sheet: 0.29 (0.21), residues: 565 loop : -0.24 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 361 HIS 0.014 0.002 HIS C 573 PHE 0.027 0.003 PHE B 593 TYR 0.020 0.002 TYR D 175 ARG 0.008 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 477 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 209 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: B 439 ARG cc_start: 0.8739 (mmt180) cc_final: 0.8521 (mmt180) REVERT: A 316 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: A 541 THR cc_start: 0.8652 (p) cc_final: 0.8451 (p) REVERT: C 154 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7379 (mt-10) REVERT: C 156 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7227 (mm-30) REVERT: C 182 GLN cc_start: 0.7481 (mt0) cc_final: 0.7176 (mt0) REVERT: C 217 PHE cc_start: 0.8479 (m-80) cc_final: 0.8180 (m-80) REVERT: C 339 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7927 (mtt180) REVERT: C 521 MET cc_start: 0.7893 (mtp) cc_final: 0.7627 (mtp) REVERT: C 561 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7208 (mtt180) REVERT: D 272 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5222 (mm-30) REVERT: D 313 TYR cc_start: 0.7928 (m-80) cc_final: 0.7576 (m-80) outliers start: 65 outliers final: 31 residues processed: 501 average time/residue: 1.3957 time to fit residues: 774.8341 Evaluate side-chains 500 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 464 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 535 SER Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 592 ASP Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 370 ASN B 443 GLN A 66 ASN A 275 ASN A 399 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 474 ASN C 554 HIS C 558 ASN C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18301 Z= 0.220 Angle : 0.570 7.609 24835 Z= 0.306 Chirality : 0.044 0.145 2753 Planarity : 0.003 0.033 3174 Dihedral : 6.041 43.673 3286 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.01 % Allowed : 15.41 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2117 helix: 0.30 (0.32), residues: 263 sheet: 0.26 (0.21), residues: 568 loop : -0.19 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 361 HIS 0.007 0.001 HIS B 268 PHE 0.016 0.002 PHE A 245 TYR 0.025 0.001 TYR D 175 ARG 0.005 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 484 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 472 TYR cc_start: 0.8334 (m-80) cc_final: 0.8059 (m-80) REVERT: C 154 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7272 (mt-10) REVERT: C 156 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7243 (mm-30) REVERT: C 217 PHE cc_start: 0.8459 (m-80) cc_final: 0.8138 (m-80) REVERT: C 288 ASP cc_start: 0.7315 (p0) cc_final: 0.7093 (p0) REVERT: C 350 MET cc_start: 0.8484 (mtt) cc_final: 0.8230 (mtp) REVERT: C 455 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 561 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7102 (mtt180) REVERT: D 123 GLN cc_start: 0.8208 (mt0) cc_final: 0.7942 (mt0) REVERT: D 154 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 237 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8101 (t) REVERT: D 313 TYR cc_start: 0.7872 (m-80) cc_final: 0.7646 (m-80) REVERT: D 315 MET cc_start: 0.7793 (mmm) cc_final: 0.7500 (mmt) REVERT: D 579 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7220 (mtm-85) outliers start: 57 outliers final: 29 residues processed: 506 average time/residue: 1.3959 time to fit residues: 782.0201 Evaluate side-chains 504 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 471 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN B 188 GLN B 268 HIS B 370 ASN A 66 ASN A 275 ASN A 399 GLN A 455 GLN C 177 ASN C 182 GLN C 189 HIS C 558 ASN C 573 HIS C 574 GLN D 341 GLN D 345 GLN D 381 GLN D 573 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18301 Z= 0.381 Angle : 0.621 8.697 24835 Z= 0.333 Chirality : 0.047 0.149 2753 Planarity : 0.004 0.039 3174 Dihedral : 5.820 44.154 3286 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.64 % Allowed : 16.36 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.17), residues: 2117 helix: 0.20 (0.31), residues: 265 sheet: 0.25 (0.21), residues: 561 loop : -0.28 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 361 HIS 0.010 0.002 HIS B 268 PHE 0.019 0.002 PHE C 527 TYR 0.019 0.002 TYR D 175 ARG 0.009 0.001 ARG C 579 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 470 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7612 (mmtm) REVERT: A 316 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: A 541 THR cc_start: 0.8620 (p) cc_final: 0.8415 (p) REVERT: C 128 CYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5235 (m) REVERT: C 154 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7456 (mt-10) REVERT: C 156 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7402 (mm-30) REVERT: C 217 PHE cc_start: 0.8438 (m-80) cc_final: 0.8164 (m-80) REVERT: C 288 ASP cc_start: 0.7368 (p0) cc_final: 0.7152 (p0) REVERT: C 339 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (mtt180) REVERT: C 350 MET cc_start: 0.8585 (mtt) cc_final: 0.8267 (mtp) REVERT: C 381 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7414 (mt0) REVERT: C 455 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7589 (mt0) REVERT: C 561 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7184 (mtt180) REVERT: D 123 GLN cc_start: 0.8206 (mt0) cc_final: 0.7983 (mt0) REVERT: D 154 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7638 (mt-10) REVERT: D 237 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8091 (t) REVERT: D 272 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.5277 (mm-30) REVERT: D 313 TYR cc_start: 0.7899 (m-80) cc_final: 0.7571 (m-80) REVERT: D 315 MET cc_start: 0.7776 (mmm) cc_final: 0.7473 (mmt) outliers start: 69 outliers final: 39 residues processed: 500 average time/residue: 1.4365 time to fit residues: 795.3885 Evaluate side-chains 515 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 467 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 128 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 526 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 543 ILE Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 268 HIS B 370 ASN A 455 GLN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18301 Z= 0.167 Angle : 0.532 9.488 24835 Z= 0.287 Chirality : 0.043 0.154 2753 Planarity : 0.003 0.035 3174 Dihedral : 5.383 46.396 3286 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.01 % Allowed : 16.89 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2117 helix: 0.54 (0.32), residues: 265 sheet: 0.44 (0.22), residues: 546 loop : -0.22 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 567 HIS 0.009 0.001 HIS B 268 PHE 0.013 0.001 PHE A 527 TYR 0.013 0.001 TYR D 175 ARG 0.006 0.000 ARG A 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 470 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7577 (mmtm) REVERT: A 316 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: C 154 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 156 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7398 (mm-30) REVERT: C 339 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7902 (mtt180) REVERT: C 561 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7048 (mtt180) REVERT: D 123 GLN cc_start: 0.8205 (mt0) cc_final: 0.7797 (mt0) REVERT: D 154 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7592 (mt-10) REVERT: D 313 TYR cc_start: 0.7829 (m-80) cc_final: 0.7626 (m-80) REVERT: D 315 MET cc_start: 0.7752 (mmm) cc_final: 0.7442 (mmt) outliers start: 57 outliers final: 29 residues processed: 493 average time/residue: 1.4046 time to fit residues: 766.6584 Evaluate side-chains 487 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 454 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 149 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 268 HIS B 370 ASN C 177 ASN C 182 GLN C 189 HIS C 215 GLN C 574 GLN D 341 GLN D 345 GLN D 381 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18301 Z= 0.374 Angle : 0.611 10.919 24835 Z= 0.326 Chirality : 0.046 0.150 2753 Planarity : 0.004 0.056 3174 Dihedral : 5.614 47.604 3286 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.11 % Allowed : 17.73 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2117 helix: 0.34 (0.31), residues: 265 sheet: 0.27 (0.22), residues: 555 loop : -0.30 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 361 HIS 0.011 0.002 HIS B 268 PHE 0.019 0.002 PHE C 527 TYR 0.016 0.002 TYR C 214 ARG 0.015 0.001 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 465 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 188 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: B 340 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7596 (mmtm) REVERT: A 316 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7892 (tt0) REVERT: C 154 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7494 (mt-10) REVERT: C 156 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 316 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7346 (tp40) REVERT: C 339 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7931 (mtt180) REVERT: C 561 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: D 123 GLN cc_start: 0.8207 (mt0) cc_final: 0.7982 (mt0) REVERT: D 154 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 237 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8086 (t) REVERT: D 272 GLU cc_start: 0.6171 (OUTLIER) cc_final: 0.5198 (mm-30) REVERT: D 313 TYR cc_start: 0.7865 (m-80) cc_final: 0.7557 (m-80) REVERT: D 315 MET cc_start: 0.7798 (mmm) cc_final: 0.7507 (mmt) outliers start: 59 outliers final: 42 residues processed: 487 average time/residue: 1.4269 time to fit residues: 767.2859 Evaluate side-chains 510 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 460 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 GLN B 268 HIS B 370 ASN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.039 18301 Z= 0.218 Angle : 0.555 11.202 24835 Z= 0.298 Chirality : 0.043 0.155 2753 Planarity : 0.003 0.033 3174 Dihedral : 5.444 48.519 3286 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.80 % Allowed : 18.31 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2117 helix: 0.52 (0.32), residues: 265 sheet: 0.38 (0.22), residues: 542 loop : -0.29 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 361 HIS 0.011 0.001 HIS B 268 PHE 0.020 0.001 PHE A 245 TYR 0.011 0.001 TYR A 472 ARG 0.009 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 457 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7582 (mmtm) REVERT: B 545 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: A 316 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: A 472 TYR cc_start: 0.8328 (m-80) cc_final: 0.7951 (m-80) REVERT: C 154 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 156 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7438 (mm-30) REVERT: C 339 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7906 (mtt180) REVERT: C 561 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: D 154 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 237 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8102 (t) REVERT: D 313 TYR cc_start: 0.7834 (m-80) cc_final: 0.7609 (m-80) REVERT: D 315 MET cc_start: 0.7785 (mmm) cc_final: 0.7508 (mmt) REVERT: D 372 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7441 (ptm-80) outliers start: 53 outliers final: 36 residues processed: 483 average time/residue: 1.5137 time to fit residues: 812.5719 Evaluate side-chains 500 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 457 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN C 177 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18301 Z= 0.214 Angle : 0.552 12.887 24835 Z= 0.294 Chirality : 0.043 0.154 2753 Planarity : 0.003 0.033 3174 Dihedral : 5.338 49.076 3286 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.43 % Allowed : 18.79 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2117 helix: 0.65 (0.32), residues: 265 sheet: 0.36 (0.22), residues: 561 loop : -0.25 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 544 HIS 0.011 0.001 HIS B 268 PHE 0.015 0.001 PHE A 527 TYR 0.010 0.001 TYR D 403 ARG 0.012 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 457 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7576 (mmtm) REVERT: B 545 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: A 316 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 472 TYR cc_start: 0.8326 (m-80) cc_final: 0.7920 (m-80) REVERT: C 154 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7601 (mt-10) REVERT: C 156 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7476 (mm-30) REVERT: C 339 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7921 (mtt180) REVERT: C 561 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.6986 (mtt180) REVERT: D 111 LYS cc_start: 0.8287 (ptmm) cc_final: 0.8006 (ptmm) REVERT: D 154 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7622 (mt-10) REVERT: D 237 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.8112 (t) REVERT: D 313 TYR cc_start: 0.7826 (m-80) cc_final: 0.7601 (m-80) REVERT: D 315 MET cc_start: 0.7776 (mmm) cc_final: 0.7499 (mmt) REVERT: D 372 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7449 (ptm-80) outliers start: 46 outliers final: 31 residues processed: 482 average time/residue: 1.4898 time to fit residues: 792.2824 Evaluate side-chains 493 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 455 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 561 ARG Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS B 370 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18301 Z= 0.205 Angle : 0.559 12.739 24835 Z= 0.299 Chirality : 0.043 0.178 2753 Planarity : 0.003 0.032 3174 Dihedral : 5.350 49.297 3286 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.37 % Allowed : 18.94 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2117 helix: 0.69 (0.32), residues: 265 sheet: 0.30 (0.22), residues: 571 loop : -0.21 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 544 HIS 0.013 0.001 HIS B 268 PHE 0.013 0.001 PHE C 527 TYR 0.015 0.001 TYR D 97 ARG 0.007 0.000 ARG A 255 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4234 Ramachandran restraints generated. 2117 Oldfield, 0 Emsley, 2117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 458 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 CYS cc_start: 0.6148 (m) cc_final: 0.5717 (m) REVERT: B 340 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7569 (mmtm) REVERT: B 545 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: A 316 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: A 472 TYR cc_start: 0.8329 (m-80) cc_final: 0.7908 (m-80) REVERT: C 339 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7917 (mtt180) REVERT: D 111 LYS cc_start: 0.8302 (ptmm) cc_final: 0.8016 (ptmm) REVERT: D 154 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 237 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (t) REVERT: D 272 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5183 (mm-30) REVERT: D 313 TYR cc_start: 0.7807 (m-80) cc_final: 0.7536 (m-80) REVERT: D 315 MET cc_start: 0.7772 (mmm) cc_final: 0.7489 (mmt) REVERT: D 372 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7491 (ptm-80) outliers start: 45 outliers final: 32 residues processed: 481 average time/residue: 1.4058 time to fit residues: 746.4383 Evaluate side-chains 491 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 452 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 455 GLN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 559 CYS Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.0570 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 188 GLN B 268 HIS B 370 ASN A 455 GLN C 177 ASN C 182 GLN C 189 HIS D 341 GLN D 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117506 restraints weight = 22336.099| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.72 r_work: 0.3439 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18301 Z= 0.327 Angle : 0.603 13.040 24835 Z= 0.321 Chirality : 0.046 0.174 2753 Planarity : 0.004 0.042 3174 Dihedral : 5.509 49.828 3286 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.48 % Allowed : 19.00 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2117 helix: 0.41 (0.31), residues: 271 sheet: 0.24 (0.21), residues: 579 loop : -0.31 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 361 HIS 0.013 0.002 HIS B 268 PHE 0.022 0.002 PHE A 245 TYR 0.014 0.002 TYR A 403 ARG 0.013 0.001 ARG C 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10675.95 seconds wall clock time: 186 minutes 36.59 seconds (11196.59 seconds total)