Starting phenix.real_space_refine on Sun Mar 17 13:50:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/03_2024/7uaf_26423_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/03_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_26423/03_2024/7uaf_26423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/03_2024/7uaf_26423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/03_2024/7uaf_26423_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaf_26423/03_2024/7uaf_26423_updated.pdb" } 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 Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 255": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B ARG 364": "NH1" <-> "NH2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B ARG 546": "NH1" <-> "NH2" Residue "B ARG 549": "NH1" <-> "NH2" Residue "B PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ARG 546": "NH1" <-> "NH2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 255": "NH1" <-> "NH2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C GLU 299": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C GLU 428": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 476": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C GLU 514": "OE1" <-> "OE2" Residue "C ARG 546": "NH1" <-> "NH2" Residue "C ARG 549": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 255": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 364": "NH1" <-> "NH2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 546": "NH1" <-> "NH2" Residue "D ARG 549": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 9.13, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 7.87 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 69 helices and 31 sheets defined 17.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 89 through 105 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 247 through 257 Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.505A pdb=" N GLU B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 89 through 105 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 536 through 538 No H-bonds generated for 'chain 'A' and resid 536 through 538' Processing helix chain 'A' and resid 547 through 550 No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 89 through 105 Processing helix chain 'C' and resid 150 through 160 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 441 through 447 removed outlier: 4.146A pdb=" N GLU C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 547 through 550 No H-bonds generated for 'chain 'C' and resid 547 through 550' Processing helix chain 'C' and resid 573 through 576 No H-bonds generated for 'chain 'C' and resid 573 through 576' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 89 through 105 Processing helix chain 'D' and resid 150 through 161 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 247 through 257 Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 441 through 447 removed outlier: 4.031A pdb=" N GLU D 446 " --> pdb=" O SER D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 536 through 538 No H-bonds generated for 'chain 'D' and resid 536 through 538' Processing helix chain 'D' and resid 573 through 577 Processing helix chain 'D' and resid 597 through 599 No H-bonds generated for 'chain 'D' and resid 597 through 599' Processing sheet with id= A, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.036A pdb=" N ILE B 79 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 120 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 139 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN B 123 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 141 " --> pdb=" O GLN B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'B' and resid 290 through 292 Processing sheet with id= D, first strand: chain 'B' and resid 327 through 331 removed outlier: 6.064A pdb=" N VAL B 362 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS B 376 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 364 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 374 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 343 through 345 Processing sheet with id= F, first strand: chain 'B' and resid 434 through 438 Processing sheet with id= G, first strand: chain 'B' and resid 466 through 472 removed outlier: 3.951A pdb=" N GLY B 466 " --> pdb=" O CYS B 489 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 571 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 484 " --> pdb=" O GLY B 569 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY B 569 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE B 486 " --> pdb=" O TRP B 567 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N TRP B 567 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 488 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N LEU B 565 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 552 through 554 Processing sheet with id= I, first strand: chain 'A' and resid 110 through 112 removed outlier: 5.958A pdb=" N ILE A 79 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 120 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN A 139 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLN A 123 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 141 " --> pdb=" O GLN A 123 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= K, first strand: chain 'A' and resid 290 through 292 Processing sheet with id= L, first strand: chain 'A' and resid 327 through 331 removed outlier: 6.171A pdb=" N VAL A 362 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS A 376 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG A 364 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 374 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 343 through 345 Processing sheet with id= N, first strand: chain 'A' and resid 434 through 438 Processing sheet with id= O, first strand: chain 'A' and resid 466 through 472 removed outlier: 3.983A pdb=" N GLY A 466 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing sheet with id= P, 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: 6.543A pdb=" N ILE C 120 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN C 139 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLN C 123 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE C 141 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 176 through 178 Processing sheet with id= R, first strand: chain 'C' and resid 290 through 292 Processing sheet with id= S, first strand: chain 'C' and resid 327 through 331 removed outlier: 6.246A pdb=" N VAL C 362 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS C 376 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG C 364 " --> pdb=" O LEU C 374 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LEU C 374 " --> pdb=" O ARG C 364 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 343 through 345 Processing sheet with id= U, first strand: chain 'C' and resid 434 through 438 Processing sheet with id= V, first strand: chain 'C' and resid 466 through 472 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= W, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= X, first strand: chain 'D' and resid 110 through 112 removed outlier: 6.008A pdb=" N ILE D 79 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 120 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN D 139 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLN D 123 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 141 " --> pdb=" O GLN D 123 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 176 through 178 Processing sheet with id= Z, first strand: chain 'D' and resid 290 through 292 Processing sheet with id= AA, first strand: chain 'D' and resid 327 through 331 removed outlier: 6.184A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 343 through 345 Processing sheet with id= AC, first strand: chain 'D' and resid 434 through 438 Processing sheet with id= AD, first strand: chain 'D' and resid 466 through 472 removed outlier: 3.863A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 571 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU D 484 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY D 569 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE D 486 " --> pdb=" O TRP D 567 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N TRP D 567 " --> pdb=" O PHE D 486 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL D 488 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N LEU D 565 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 551 through 554 442 hydrogen bonds defined for protein. 1149 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: 6.02 Time building geometry restraints manager: 8.35 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: 97.12 - 104.71: 278 104.71 - 112.29: 7655 112.29 - 119.88: 8176 119.88 - 127.47: 8513 127.47 - 135.06: 213 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: 10014 3.03 - 3.65: 25570 3.65 - 4.28: 44773 4.28 - 4.90: 70537 Nonbonded interactions: 150932 Sorted by model distance: nonbonded pdb=" O CYS D 128 " pdb=" O6 M6X D 701 " model vdw 1.783 2.440 nonbonded pdb=" OH TYR B 214 " pdb=" O3 M6X B 701 " model vdw 1.855 2.440 nonbonded pdb=" O CYS D 128 " pdb=" N2 M6X D 701 " model vdw 1.856 2.520 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 2.440 ... (remaining 150927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.440 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 52.060 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.840 ------------------------------------------------------------------------------- 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= 0.784 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 : 2.171 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: 1.3262 time to fit residues: 832.8070 Evaluate side-chains 469 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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: 6.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN B 145 GLN B 215 GLN B 307 GLN B 341 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18301 Z= 0.203 Angle : 0.627 9.462 24835 Z= 0.340 Chirality : 0.047 0.207 2753 Planarity : 0.003 0.033 3174 Dihedral : 9.074 68.004 3286 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.16 % Allowed : 10.45 % Favored : 87.39 % 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: 0.27 (0.18), residues: 2117 helix: -0.27 (0.31), residues: 264 sheet: 0.48 (0.20), residues: 571 loop : 0.25 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 361 HIS 0.008 0.001 HIS B 155 PHE 0.022 0.002 PHE C 245 TYR 0.020 0.002 TYR D 97 ARG 0.005 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 508 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 467 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6963 (pt0) REVERT: A 316 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: A 461 ASN cc_start: 0.7747 (p0) cc_final: 0.7367 (p0) REVERT: C 154 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 156 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6959 (mm-30) REVERT: C 217 PHE cc_start: 0.8488 (m-80) cc_final: 0.8164 (m-80) REVERT: C 251 GLU cc_start: 0.6954 (tt0) cc_final: 0.6622 (tt0) REVERT: C 279 MET cc_start: 0.4683 (mtt) cc_final: 0.4365 (mtt) REVERT: D 113 TYR cc_start: 0.8121 (t80) cc_final: 0.7813 (t80) REVERT: D 154 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7434 (mt-10) REVERT: D 207 ASP cc_start: 0.6800 (t0) cc_final: 0.6531 (t0) REVERT: D 242 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6652 (mtt90) REVERT: D 313 TYR cc_start: 0.7863 (m-80) cc_final: 0.7629 (m-80) outliers start: 41 outliers final: 16 residues processed: 484 average time/residue: 1.3947 time to fit residues: 746.5872 Evaluate side-chains 476 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 458 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 501 VAL Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 574 GLN Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 538 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 124 GLN B 145 GLN B 341 GLN B 370 ASN B 413 GLN 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 D 399 GLN D 558 ASN D 573 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2401 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= 0.549 Angle : 0.721 8.251 24835 Z= 0.384 Chirality : 0.052 0.181 2753 Planarity : 0.005 0.059 3174 Dihedral : 7.295 43.138 3286 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.64 % Allowed : 13.09 % Favored : 83.27 % 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: -0.04 (0.17), residues: 2117 helix: -0.28 (0.31), residues: 260 sheet: 0.40 (0.21), residues: 579 loop : -0.08 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 361 HIS 0.014 0.003 HIS C 573 PHE 0.027 0.003 PHE B 593 TYR 0.022 0.002 TYR D 175 ARG 0.012 0.001 ARG D 579 *********************** 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 554 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 485 time to evaluate : 2.096 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 66 ASN cc_start: 0.8140 (OUTLIER) cc_final: 0.7828 (p0) REVERT: B 266 LEU cc_start: 0.8643 (tp) cc_final: 0.8436 (tt) REVERT: B 364 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7808 (ptp-110) REVERT: A 111 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7703 (pttp) REVERT: A 316 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 154 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7433 (mt-10) REVERT: C 217 PHE cc_start: 0.8473 (m-80) cc_final: 0.8190 (m-80) REVERT: C 251 GLU cc_start: 0.6974 (tt0) cc_final: 0.6653 (tt0) REVERT: C 279 MET cc_start: 0.4823 (mtt) cc_final: 0.4518 (mtp) REVERT: C 561 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7190 (mtt180) REVERT: D 272 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5241 (mm-30) REVERT: D 313 TYR cc_start: 0.7919 (m-80) cc_final: 0.7590 (m-80) REVERT: D 502 GLU cc_start: 0.6386 (tt0) cc_final: 0.6084 (tt0) REVERT: D 531 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7455 (mmmm) REVERT: D 579 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.7032 (mtt-85) outliers start: 69 outliers final: 43 residues processed: 509 average time/residue: 1.3623 time to fit residues: 768.6294 Evaluate side-chains 517 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 468 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 89 LEU 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 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 66 ASN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 261 THR 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 362 VAL Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 531 LYS 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 74 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 353 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 579 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 203 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN B 124 GLN B 268 HIS B 370 ASN B 392 HIS B 443 GLN B 574 GLN A 66 ASN A 275 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS C 474 ASN C 554 HIS C 573 HIS C 574 GLN D 341 GLN D 345 GLN D 558 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2645 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= 0.194 Angle : 0.549 6.860 24835 Z= 0.294 Chirality : 0.044 0.157 2753 Planarity : 0.003 0.037 3174 Dihedral : 6.011 42.470 3286 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.27 % Allowed : 15.09 % Favored : 81.64 % 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: 0.07 (0.18), residues: 2117 helix: 0.16 (0.32), residues: 264 sheet: 0.35 (0.21), residues: 580 loop : -0.04 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 361 HIS 0.008 0.001 HIS B 268 PHE 0.015 0.001 PHE A 245 TYR 0.025 0.001 TYR D 175 ARG 0.009 0.000 ARG D 579 *********************** 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 540 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 478 time to evaluate : 1.925 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: 0.8073 (OUTLIER) cc_final: 0.7597 (mmtm) REVERT: B 364 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7839 (ptp-110) REVERT: A 316 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 472 TYR cc_start: 0.8296 (m-80) cc_final: 0.8026 (m-80) REVERT: C 154 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 156 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7212 (mm-30) REVERT: C 157 ILE cc_start: 0.7853 (mt) cc_final: 0.7652 (mm) REVERT: C 214 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: C 215 GLN cc_start: 0.7425 (pt0) cc_final: 0.7195 (pt0) REVERT: C 217 PHE cc_start: 0.8472 (m-80) cc_final: 0.8144 (m-80) REVERT: C 251 GLU cc_start: 0.6948 (tt0) cc_final: 0.6635 (tt0) REVERT: C 279 MET cc_start: 0.4801 (mtt) cc_final: 0.4547 (mtp) REVERT: C 339 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7899 (mtt180) REVERT: C 350 MET cc_start: 0.8543 (mtt) cc_final: 0.8178 (mtp) REVERT: C 455 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: C 561 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7143 (mtt180) REVERT: D 123 GLN cc_start: 0.8197 (mt0) cc_final: 0.7979 (mt0) REVERT: D 153 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 154 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 313 TYR cc_start: 0.7844 (m-80) cc_final: 0.7617 (m-80) REVERT: D 315 MET cc_start: 0.7804 (mmm) cc_final: 0.7513 (mmt) outliers start: 62 outliers final: 27 residues processed: 505 average time/residue: 1.3586 time to fit residues: 760.7016 Evaluate side-chains 498 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 464 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 THR Chi-restraints excluded: chain A residue 237 SER 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 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 265 LEU 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 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 561 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 577 LYS 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: 4.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 140 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 0.0370 chunk 51 optimal weight: 0.8980 overall best weight: 0.9318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 66 ASN A 474 ASN C 182 GLN C 189 HIS C 574 GLN D 341 GLN D 345 GLN D 558 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18301 Z= 0.217 Angle : 0.543 7.518 24835 Z= 0.291 Chirality : 0.043 0.148 2753 Planarity : 0.003 0.035 3174 Dihedral : 5.644 43.426 3286 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.48 % Allowed : 16.15 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2117 helix: 0.28 (0.32), residues: 264 sheet: 0.33 (0.21), residues: 584 loop : -0.05 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 361 HIS 0.008 0.001 HIS B 268 PHE 0.018 0.002 PHE A 245 TYR 0.019 0.001 TYR D 175 ARG 0.015 0.000 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 532 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 466 time to evaluate : 2.112 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: 0.8076 (OUTLIER) cc_final: 0.7598 (mmtm) REVERT: A 287 THR cc_start: 0.8055 (t) cc_final: 0.7853 (p) REVERT: A 316 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: C 128 CYS cc_start: 0.5904 (m) cc_final: 0.5319 (m) REVERT: C 154 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 156 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7189 (mm-30) REVERT: C 214 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7892 (m-10) REVERT: C 215 GLN cc_start: 0.7450 (pt0) cc_final: 0.7193 (pt0) REVERT: C 217 PHE cc_start: 0.8468 (m-80) cc_final: 0.8131 (m-80) REVERT: C 251 GLU cc_start: 0.6948 (tt0) cc_final: 0.6637 (tt0) REVERT: C 279 MET cc_start: 0.4809 (mtt) cc_final: 0.4568 (mtp) REVERT: C 339 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7891 (mtt180) REVERT: C 561 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7104 (mtt180) REVERT: D 123 GLN cc_start: 0.8199 (mt0) cc_final: 0.7989 (mt0) REVERT: D 153 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7663 (mt) REVERT: D 154 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 313 TYR cc_start: 0.7840 (m-80) cc_final: 0.7621 (m-80) REVERT: D 315 MET cc_start: 0.7797 (mmm) cc_final: 0.7486 (mmt) outliers start: 66 outliers final: 34 residues processed: 489 average time/residue: 1.3680 time to fit residues: 739.8656 Evaluate side-chains 501 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 461 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 GLU 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 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 A residue 66 ASN Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 228 ILE 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 543 ILE Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 214 TYR 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 444 VAL Chi-restraints excluded: chain C residue 511 LEU 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 74 ARG Chi-restraints excluded: chain D residue 153 ILE 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 345 GLN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU 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: 3.9990 chunk 183 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 119 optimal weight: 0.0060 chunk 50 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 145 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 66 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18301 Z= 0.349 Angle : 0.582 6.933 24835 Z= 0.312 Chirality : 0.046 0.142 2753 Planarity : 0.004 0.042 3174 Dihedral : 5.621 43.990 3286 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.43 % Allowed : 17.20 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2117 helix: 0.22 (0.32), residues: 264 sheet: 0.33 (0.22), residues: 554 loop : -0.12 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 361 HIS 0.011 0.001 HIS B 268 PHE 0.019 0.002 PHE A 245 TYR 0.015 0.002 TYR D 175 ARG 0.010 0.001 ARG C 579 *********************** 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 526 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 461 time to evaluate : 1.930 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: 0.8082 (OUTLIER) cc_final: 0.7597 (mmtm) REVERT: A 316 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: C 154 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7280 (mt-10) REVERT: C 156 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7206 (mm-30) REVERT: C 214 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7790 (m-10) REVERT: C 217 PHE cc_start: 0.8467 (m-80) cc_final: 0.8183 (m-80) REVERT: C 251 GLU cc_start: 0.6959 (tt0) cc_final: 0.6652 (tt0) REVERT: C 279 MET cc_start: 0.4755 (mtt) cc_final: 0.4539 (mtp) REVERT: C 339 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7923 (mtt180) REVERT: C 561 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7157 (mtt180) REVERT: D 123 GLN cc_start: 0.8210 (mt0) cc_final: 0.7996 (mt0) REVERT: D 153 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7735 (mt) REVERT: D 154 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 313 TYR cc_start: 0.7861 (m-80) cc_final: 0.7607 (m-80) REVERT: D 315 MET cc_start: 0.7816 (mmm) cc_final: 0.7493 (mmt) REVERT: D 353 SER cc_start: 0.8460 (OUTLIER) cc_final: 0.8210 (p) outliers start: 65 outliers final: 39 residues processed: 490 average time/residue: 1.3603 time to fit residues: 739.4631 Evaluate side-chains 503 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 457 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 362 VAL 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 591 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 237 SER 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 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 214 TYR 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 444 VAL Chi-restraints excluded: chain C residue 511 LEU 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 74 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 237 SER 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 353 SER Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 452 ASP Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 577 LYS 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: 0.3980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 124 GLN B 188 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN C 182 GLN C 189 HIS D 341 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18301 Z= 0.203 Angle : 0.517 6.371 24835 Z= 0.278 Chirality : 0.043 0.140 2753 Planarity : 0.003 0.035 3174 Dihedral : 5.370 45.648 3286 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.17 % Allowed : 17.63 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2117 helix: 0.42 (0.33), residues: 264 sheet: 0.38 (0.22), residues: 555 loop : -0.09 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 361 HIS 0.010 0.001 HIS B 268 PHE 0.023 0.001 PHE A 245 TYR 0.013 0.001 TYR C 420 ARG 0.008 0.000 ARG D 579 *********************** 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 521 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 461 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7587 (mmtm) REVERT: A 316 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: C 154 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7080 (mt-10) REVERT: C 156 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 214 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: C 215 GLN cc_start: 0.7478 (pt0) cc_final: 0.7249 (pt0) REVERT: C 217 PHE cc_start: 0.8451 (m-80) cc_final: 0.8147 (m-80) REVERT: C 251 GLU cc_start: 0.6946 (tt0) cc_final: 0.6634 (tt0) REVERT: C 279 MET cc_start: 0.4806 (mtt) cc_final: 0.4582 (mtp) REVERT: C 561 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7159 (mtt180) REVERT: D 74 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.5355 (mpt180) REVERT: D 123 GLN cc_start: 0.8203 (mt0) cc_final: 0.7996 (mt0) REVERT: D 153 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7651 (mt) REVERT: D 154 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7721 (mt-10) REVERT: D 313 TYR cc_start: 0.7822 (m-80) cc_final: 0.7580 (m-80) REVERT: D 315 MET cc_start: 0.7785 (mmm) cc_final: 0.7446 (mmt) REVERT: D 353 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8213 (p) outliers start: 60 outliers final: 32 residues processed: 492 average time/residue: 1.3679 time to fit residues: 744.9656 Evaluate side-chains 486 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 447 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 362 VAL 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 A residue 228 ILE 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 362 VAL 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 543 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 214 TYR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER 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 74 ARG Chi-restraints excluded: chain D residue 153 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 288 ASP Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU 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: 4.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 124 GLN B 188 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN A 573 HIS C 139 GLN C 182 GLN C 189 HIS D 341 GLN D 345 GLN D 513 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18301 Z= 0.390 Angle : 0.599 7.439 24835 Z= 0.320 Chirality : 0.046 0.142 2753 Planarity : 0.004 0.036 3174 Dihedral : 5.583 46.408 3286 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.22 % Allowed : 18.05 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2117 helix: 0.24 (0.32), residues: 264 sheet: 0.31 (0.22), residues: 552 loop : -0.21 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 361 HIS 0.012 0.002 HIS B 268 PHE 0.021 0.002 PHE A 245 TYR 0.016 0.002 TYR D 403 ARG 0.012 0.001 ARG C 69 *********************** 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 519 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 458 time to evaluate : 1.963 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: 0.8081 (OUTLIER) cc_final: 0.7599 (mmtm) REVERT: B 428 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: A 316 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: C 154 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7292 (mt-10) REVERT: C 156 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7207 (mm-30) REVERT: C 214 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: C 217 PHE cc_start: 0.8451 (m-80) cc_final: 0.8159 (m-80) REVERT: C 251 GLU cc_start: 0.6961 (tt0) cc_final: 0.6657 (tt0) REVERT: C 279 MET cc_start: 0.4782 (mtt) cc_final: 0.4573 (mtp) REVERT: C 561 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7210 (mtt180) REVERT: D 123 GLN cc_start: 0.8216 (mt0) cc_final: 0.8005 (mt0) REVERT: D 153 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7830 (mt) REVERT: D 154 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 272 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5156 (mm-30) REVERT: D 313 TYR cc_start: 0.7864 (m-80) cc_final: 0.7573 (m-80) REVERT: D 315 MET cc_start: 0.7819 (mmm) cc_final: 0.7496 (mmt) REVERT: D 353 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (p) outliers start: 61 outliers final: 39 residues processed: 483 average time/residue: 1.3609 time to fit residues: 726.9991 Evaluate side-chains 502 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 455 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 362 VAL Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 248 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 362 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 425 THR 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 214 TYR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER 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 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 153 ILE Chi-restraints excluded: chain D residue 237 SER 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 353 SER Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 577 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 0.9990 chunk 188 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 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 B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN C 182 GLN C 189 HIS D 341 GLN D 345 GLN D 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18301 Z= 0.196 Angle : 0.517 7.309 24835 Z= 0.277 Chirality : 0.042 0.143 2753 Planarity : 0.003 0.039 3174 Dihedral : 5.308 46.543 3286 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.22 % Allowed : 19.16 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2117 helix: 0.45 (0.33), residues: 264 sheet: 0.42 (0.22), residues: 547 loop : -0.17 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 361 HIS 0.012 0.001 HIS B 268 PHE 0.027 0.001 PHE A 245 TYR 0.013 0.001 TYR A 113 ARG 0.008 0.000 ARG C 579 *********************** 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 506 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 464 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7583 (mmtm) REVERT: B 397 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6594 (mm-30) REVERT: B 428 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: A 316 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: C 154 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7333 (mt-10) REVERT: C 156 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7190 (mm-30) REVERT: C 214 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7958 (m-10) REVERT: C 215 GLN cc_start: 0.7513 (pt0) cc_final: 0.7115 (pt0) REVERT: C 217 PHE cc_start: 0.8424 (m-80) cc_final: 0.8103 (m-80) REVERT: C 251 GLU cc_start: 0.6944 (tt0) cc_final: 0.6635 (tt0) REVERT: C 279 MET cc_start: 0.4819 (mtt) cc_final: 0.4602 (mtp) REVERT: C 561 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7107 (mtt180) REVERT: D 123 GLN cc_start: 0.8207 (mt0) cc_final: 0.8004 (mt0) REVERT: D 153 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7641 (mt) REVERT: D 154 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7659 (mt-10) REVERT: D 313 TYR cc_start: 0.7813 (m-80) cc_final: 0.7582 (m-80) REVERT: D 315 MET cc_start: 0.7784 (mmm) cc_final: 0.7446 (mmt) outliers start: 42 outliers final: 27 residues processed: 484 average time/residue: 1.4115 time to fit residues: 756.4711 Evaluate side-chains 491 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 458 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN 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 428 GLU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 425 THR 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 214 TYR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER 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 153 ILE Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 5.9990 chunk 122 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 193 optimal weight: 0.0050 chunk 167 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.0596 ------------------------------------------------------------------------------- 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 B 399 GLN B 443 GLN B 574 GLN A 455 GLN C 139 GLN C 182 GLN C 189 HIS D 341 GLN D 345 GLN D 519 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18301 Z= 0.237 Angle : 0.538 8.801 24835 Z= 0.288 Chirality : 0.043 0.166 2753 Planarity : 0.003 0.034 3174 Dihedral : 5.295 46.377 3286 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.11 % Allowed : 19.42 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2117 helix: 0.45 (0.33), residues: 264 sheet: 0.43 (0.22), residues: 547 loop : -0.17 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 361 HIS 0.013 0.001 HIS B 268 PHE 0.018 0.002 PHE C 163 TYR 0.013 0.001 TYR C 420 ARG 0.008 0.000 ARG C 579 ********************** 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 505 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 465 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7579 (mmtm) REVERT: B 397 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6602 (mm-30) REVERT: B 428 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6958 (mt-10) REVERT: A 316 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 154 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7321 (mt-10) REVERT: C 156 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7180 (mm-30) REVERT: C 214 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7981 (m-10) REVERT: C 215 GLN cc_start: 0.7525 (pt0) cc_final: 0.7236 (pt0) REVERT: C 217 PHE cc_start: 0.8427 (m-80) cc_final: 0.8109 (m-80) REVERT: C 251 GLU cc_start: 0.6947 (tt0) cc_final: 0.6642 (tt0) REVERT: C 279 MET cc_start: 0.4764 (mtt) cc_final: 0.4557 (mtp) REVERT: C 561 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7085 (mtt180) REVERT: D 123 GLN cc_start: 0.8214 (mt0) cc_final: 0.8006 (mt0) REVERT: D 153 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7639 (mt) REVERT: D 154 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 313 TYR cc_start: 0.7815 (m-80) cc_final: 0.7577 (m-80) REVERT: D 315 MET cc_start: 0.7801 (mmm) cc_final: 0.7462 (mmt) outliers start: 40 outliers final: 31 residues processed: 484 average time/residue: 1.3808 time to fit residues: 738.9684 Evaluate side-chains 499 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 462 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 188 GLN 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 362 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 543 ILE Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain A residue 228 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 362 VAL Chi-restraints excluded: chain A residue 425 THR 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 214 TYR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 353 SER 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 153 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 387 ASN Chi-restraints excluded: chain D residue 389 LYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 484 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 268 HIS B 370 ASN B 443 GLN B 574 GLN A 455 GLN C 177 ASN C 182 GLN C 189 HIS D 341 GLN D 345 GLN D 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.118031 restraints weight = 22411.039| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.71 r_work: 0.3451 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 18301 Z= 0.266 Angle : 0.731 59.157 24835 Z= 0.414 Chirality : 0.044 0.387 2753 Planarity : 0.004 0.036 3174 Dihedral : 5.294 46.225 3286 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.27 % Allowed : 19.26 % Favored : 78.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2117 helix: 0.45 (0.33), residues: 264 sheet: 0.43 (0.22), residues: 547 loop : -0.17 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 361 HIS 0.012 0.001 HIS B 268 PHE 0.017 0.002 PHE C 163 TYR 0.012 0.001 TYR C 420 ARG 0.008 0.000 ARG C 579 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10329.30 seconds wall clock time: 181 minutes 26.33 seconds (10886.33 seconds total)