Starting phenix.real_space_refine on Sat Mar 16 03:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfh_22853/03_2024/7kfh_22853.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 8601 2.51 5 N 2271 2.21 5 O 2655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "D TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "E TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "F TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13575 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1793 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "G" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "B" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1793 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "H" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "C" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1793 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 818 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 4, 'TRANS': 90} Chain: "I" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1026 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "B" 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: "C" 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 Time building chain proxies: 7.40, per 1000 atoms: 0.55 Number of scatterers: 13575 At special positions: 0 Unit cell: (118.45, 123.6, 123.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2655 8.00 N 2271 7.00 C 8601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 238 " " NAG A 402 " - " ASN A 268 " " NAG A 403 " - " ASN A 228 " " NAG B 401 " - " ASN B 238 " " NAG B 402 " - " ASN B 268 " " NAG B 403 " - " ASN B 228 " " NAG C 401 " - " ASN C 238 " " NAG C 402 " - " ASN C 268 " " NAG C 403 " - " ASN C 228 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.4 seconds 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3066 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 17.3% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'A' and resid 278 through 282 removed outlier: 4.481A pdb=" N ASP A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 32 Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 278 through 282 removed outlier: 4.483A pdb=" N ASP B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 32 Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'C' and resid 278 through 282 removed outlier: 4.482A pdb=" N ASP C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 32 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.739A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.700A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 544 through 549 removed outlier: 6.313A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 114 removed outlier: 6.273A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG A 136 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR A 217 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 10.057A pdb=" N ASP A 237 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER G 112 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.217A pdb=" N LEU J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.146A pdb=" N PHE G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.701A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 544 through 549 removed outlier: 6.311A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AB5, first strand: chain 'B' and resid 105 through 114 removed outlier: 6.274A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 136 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR B 217 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N ASP B 237 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER H 112 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.217A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.145A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.700A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 544 through 549 removed outlier: 6.313A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AC6, first strand: chain 'C' and resid 105 through 114 removed outlier: 6.273A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG C 136 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 14.147A pdb=" N THR C 217 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ASP C 237 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER I 112 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.216A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.146A pdb=" N PHE I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 549 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2776 1.32 - 1.45: 4283 1.45 - 1.59: 6703 1.59 - 1.72: 62 1.72 - 1.85: 60 Bond restraints: 13884 Sorted by residual: bond pdb=" CB HIS D 549 " pdb=" CG HIS D 549 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.11e+01 bond pdb=" CB HIS F 549 " pdb=" CG HIS F 549 " ideal model delta sigma weight residual 1.497 1.398 0.099 1.40e-02 5.10e+03 5.02e+01 bond pdb=" CB HIS E 549 " pdb=" CG HIS E 549 " ideal model delta sigma weight residual 1.497 1.398 0.099 1.40e-02 5.10e+03 4.95e+01 bond pdb=" CZ2 TRP F 597 " pdb=" CH2 TRP F 597 " ideal model delta sigma weight residual 1.368 1.490 -0.122 1.90e-02 2.77e+03 4.11e+01 bond pdb=" CZ2 TRP E 597 " pdb=" CH2 TRP E 597 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.08e+01 ... (remaining 13879 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.54: 558 106.54 - 113.47: 6991 113.47 - 120.40: 5996 120.40 - 127.33: 5163 127.33 - 134.26: 138 Bond angle restraints: 18846 Sorted by residual: angle pdb=" N PHE I 55 " pdb=" CA PHE I 55 " pdb=" C PHE I 55 " ideal model delta sigma weight residual 113.97 102.49 11.48 1.28e+00 6.10e-01 8.04e+01 angle pdb=" N PHE G 55 " pdb=" CA PHE G 55 " pdb=" C PHE G 55 " ideal model delta sigma weight residual 113.97 102.56 11.41 1.28e+00 6.10e-01 7.95e+01 angle pdb=" N PHE H 55 " pdb=" CA PHE H 55 " pdb=" C PHE H 55 " ideal model delta sigma weight residual 113.97 102.60 11.37 1.28e+00 6.10e-01 7.89e+01 angle pdb=" N SER A 41 " pdb=" CA SER A 41 " pdb=" C SER A 41 " ideal model delta sigma weight residual 114.12 102.22 11.90 1.39e+00 5.18e-01 7.33e+01 angle pdb=" N SER C 41 " pdb=" CA SER C 41 " pdb=" C SER C 41 " ideal model delta sigma weight residual 114.12 102.24 11.88 1.39e+00 5.18e-01 7.30e+01 ... (remaining 18841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 8313 21.15 - 42.30: 150 42.30 - 63.45: 63 63.45 - 84.60: 35 84.60 - 105.75: 16 Dihedral angle restraints: 8577 sinusoidal: 3756 harmonic: 4821 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N PRO H 101 " pdb=" CA PRO H 101 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO G 100 " pdb=" C PRO G 100 " pdb=" N PRO G 101 " pdb=" CA PRO G 101 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO I 100 " pdb=" C PRO I 100 " pdb=" N PRO I 101 " pdb=" CA PRO I 101 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 8574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1667 0.113 - 0.225: 378 0.225 - 0.338: 64 0.338 - 0.451: 39 0.451 - 0.563: 9 Chirality restraints: 2157 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 2154 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 238 " 0.096 2.00e-02 2.50e+03 1.02e-01 1.30e+02 pdb=" CG ASN B 238 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN B 238 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 238 " -0.160 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.096 2.00e-02 2.50e+03 1.02e-01 1.29e+02 pdb=" CG ASN A 238 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.096 2.00e-02 2.50e+03 1.01e-01 1.29e+02 pdb=" CG ASN C 238 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.160 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.122 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4601 2.87 - 3.38: 11831 3.38 - 3.88: 22877 3.88 - 4.39: 26253 4.39 - 4.90: 43569 Nonbonded interactions: 109131 Sorted by model distance: nonbonded pdb=" N SER C 41 " pdb=" N THR C 42 " model vdw 2.360 2.560 nonbonded pdb=" N SER B 41 " pdb=" N THR B 42 " model vdw 2.362 2.560 nonbonded pdb=" N SER A 41 " pdb=" N THR A 42 " model vdw 2.362 2.560 nonbonded pdb=" N PHE I 55 " pdb=" N GLY I 56 " model vdw 2.411 2.560 nonbonded pdb=" N PHE H 55 " pdb=" N GLY H 56 " model vdw 2.412 2.560 ... (remaining 109126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 7.360 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.610 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.021 0.122 13884 Z= 1.397 Angle : 1.757 11.901 18846 Z= 1.165 Chirality : 0.114 0.563 2157 Planarity : 0.008 0.045 2385 Dihedral : 11.997 105.755 5466 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.80 % Favored : 97.84 % Rotamer: Outliers : 0.21 % Allowed : 0.99 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1665 helix: 1.13 (0.31), residues: 159 sheet: 0.97 (0.21), residues: 594 loop : 0.65 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP L 36 HIS 0.005 0.002 HIS F 516 PHE 0.026 0.006 PHE J 84 TYR 0.060 0.009 TYR H 60 ARG 0.008 0.001 ARG K 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 383 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8154 (m-30) cc_final: 0.7343 (m-30) REVERT: A 258 GLU cc_start: 0.7972 (tp30) cc_final: 0.7394 (tp30) REVERT: D 549 HIS cc_start: 0.8104 (p-80) cc_final: 0.7833 (t-170) REVERT: D 581 THR cc_start: 0.9521 (m) cc_final: 0.9132 (p) REVERT: D 596 ARG cc_start: 0.7704 (mtp-110) cc_final: 0.7482 (mtt-85) REVERT: G 48 MET cc_start: 0.7713 (mtp) cc_final: 0.7387 (mtp) REVERT: G 78 THR cc_start: 0.8456 (m) cc_final: 0.7838 (p) REVERT: G 83 LEU cc_start: 0.7106 (tp) cc_final: 0.6651 (tp) REVERT: G 108 TRP cc_start: 0.8336 (p-90) cc_final: 0.8120 (p90) REVERT: G 114 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7553 (mtmm) REVERT: B 55 ASP cc_start: 0.8164 (m-30) cc_final: 0.7106 (m-30) REVERT: K 37 TYR cc_start: 0.5217 (m-80) cc_final: 0.4306 (m-80) REVERT: K 47 LEU cc_start: 0.3496 (tp) cc_final: 0.3250 (tt) REVERT: K 48 LEU cc_start: 0.8217 (mt) cc_final: 0.7862 (mt) REVERT: E 549 HIS cc_start: 0.8025 (p-80) cc_final: 0.7708 (t-170) REVERT: E 550 ASN cc_start: 0.9131 (t0) cc_final: 0.8599 (t0) REVERT: E 581 THR cc_start: 0.9515 (m) cc_final: 0.9246 (p) REVERT: H 48 MET cc_start: 0.7477 (mtp) cc_final: 0.7242 (mtp) REVERT: H 78 THR cc_start: 0.8201 (m) cc_final: 0.7608 (p) REVERT: H 81 MET cc_start: 0.7905 (ttp) cc_final: 0.7634 (tmm) REVERT: H 83 LEU cc_start: 0.7587 (tp) cc_final: 0.7106 (tp) REVERT: H 114 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7589 (ptpt) REVERT: C 109 TYR cc_start: 0.9053 (m-80) cc_final: 0.8765 (m-80) REVERT: C 258 GLU cc_start: 0.7918 (tp30) cc_final: 0.7394 (tp30) REVERT: L 37 TYR cc_start: 0.5533 (m-80) cc_final: 0.4804 (m-80) REVERT: F 550 ASN cc_start: 0.8993 (t0) cc_final: 0.8786 (t0) REVERT: F 581 THR cc_start: 0.9508 (m) cc_final: 0.9009 (p) REVERT: F 596 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7518 (mtt-85) REVERT: F 597 TRP cc_start: 0.6861 (t-100) cc_final: 0.6339 (t-100) REVERT: I 78 THR cc_start: 0.7994 (m) cc_final: 0.7360 (p) REVERT: I 83 LEU cc_start: 0.7483 (tp) cc_final: 0.7013 (tp) REVERT: I 94 TYR cc_start: 0.5017 (m-80) cc_final: 0.4622 (m-10) REVERT: I 114 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7520 (ptpt) outliers start: 3 outliers final: 3 residues processed: 386 average time/residue: 0.3190 time to fit residues: 166.2520 Evaluate side-chains 229 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 226 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain C residue 238 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN J 39 GLN G 39 GLN K 39 GLN H 39 GLN C 44 GLN F 549 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13884 Z= 0.238 Angle : 0.668 7.857 18846 Z= 0.357 Chirality : 0.045 0.214 2157 Planarity : 0.004 0.032 2385 Dihedral : 8.923 74.097 2463 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.22 % Favored : 97.60 % Rotamer: Outliers : 2.68 % Allowed : 7.42 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.86 (0.20), residues: 1665 helix: 1.92 (0.34), residues: 162 sheet: 0.74 (0.21), residues: 615 loop : 0.30 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 47 HIS 0.002 0.001 HIS E 549 PHE 0.023 0.002 PHE J 72 TYR 0.016 0.002 TYR L 50 ARG 0.008 0.001 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.8162 (m-30) cc_final: 0.7541 (m-30) REVERT: G 60 TYR cc_start: 0.5895 (m-80) cc_final: 0.5636 (m-80) REVERT: G 81 MET cc_start: 0.7928 (tmm) cc_final: 0.7430 (tmm) REVERT: G 106 ARG cc_start: 0.8412 (mtp-110) cc_final: 0.8111 (ttm110) REVERT: G 114 LYS cc_start: 0.8251 (ttpt) cc_final: 0.7699 (mtmm) REVERT: B 55 ASP cc_start: 0.7701 (m-30) cc_final: 0.7481 (m-30) REVERT: E 597 TRP cc_start: 0.6593 (t-100) cc_final: 0.6360 (t-100) REVERT: H 48 MET cc_start: 0.7127 (mtp) cc_final: 0.6752 (mtp) REVERT: H 78 THR cc_start: 0.7822 (m) cc_final: 0.7495 (p) REVERT: H 81 MET cc_start: 0.8023 (ttp) cc_final: 0.7642 (tmm) REVERT: H 114 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7502 (mtmm) REVERT: C 55 ASP cc_start: 0.7923 (m-30) cc_final: 0.7277 (m-30) REVERT: L 37 TYR cc_start: 0.5091 (m-80) cc_final: 0.4674 (m-80) REVERT: F 545 GLU cc_start: 0.8488 (pm20) cc_final: 0.8186 (pm20) REVERT: F 550 ASN cc_start: 0.9248 (t0) cc_final: 0.8922 (t0) REVERT: I 78 THR cc_start: 0.7684 (m) cc_final: 0.7467 (p) REVERT: I 114 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7508 (mtmm) outliers start: 38 outliers final: 20 residues processed: 276 average time/residue: 0.2909 time to fit residues: 111.4933 Evaluate side-chains 235 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 83 ASP Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 593 LEU Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain F residue 593 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 100 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 50 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN H 59 ASN L 39 GLN I 39 GLN I 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13884 Z= 0.208 Angle : 0.605 10.433 18846 Z= 0.313 Chirality : 0.043 0.153 2157 Planarity : 0.004 0.031 2385 Dihedral : 7.903 61.290 2463 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.46 % Favored : 97.36 % Rotamer: Outliers : 3.60 % Allowed : 9.04 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.75 (0.20), residues: 1665 helix: 2.25 (0.38), residues: 162 sheet: 0.77 (0.21), residues: 612 loop : 0.04 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS F 549 PHE 0.019 0.002 PHE I 29 TYR 0.019 0.002 TYR I 117 ARG 0.009 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 THR cc_start: 0.9455 (m) cc_final: 0.9088 (p) REVERT: G 60 TYR cc_start: 0.6027 (m-80) cc_final: 0.5728 (m-80) REVERT: G 81 MET cc_start: 0.8247 (tmm) cc_final: 0.7542 (tmm) REVERT: G 114 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7652 (mtmm) REVERT: H 65 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7990 (mm-40) REVERT: H 73 ASP cc_start: 0.4966 (p0) cc_final: 0.4719 (p0) REVERT: H 78 THR cc_start: 0.8013 (m) cc_final: 0.7724 (p) REVERT: H 81 MET cc_start: 0.7924 (ttp) cc_final: 0.7689 (tmm) REVERT: H 114 LYS cc_start: 0.8215 (ttpt) cc_final: 0.7514 (mtmm) REVERT: C 55 ASP cc_start: 0.7604 (m-30) cc_final: 0.7376 (m-30) REVERT: L 48 LEU cc_start: 0.7521 (mt) cc_final: 0.7237 (mp) REVERT: I 73 ASP cc_start: 0.5018 (p0) cc_final: 0.4702 (p0) REVERT: I 81 MET cc_start: 0.7940 (tmm) cc_final: 0.7727 (tmm) REVERT: I 114 LYS cc_start: 0.8276 (ttpt) cc_final: 0.7504 (mtmm) outliers start: 51 outliers final: 26 residues processed: 270 average time/residue: 0.2910 time to fit residues: 111.5920 Evaluate side-chains 226 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 595 GLN Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 156 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN I 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13884 Z= 0.182 Angle : 0.562 7.061 18846 Z= 0.286 Chirality : 0.043 0.160 2157 Planarity : 0.004 0.057 2385 Dihedral : 6.816 46.800 2463 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.46 % Favored : 97.36 % Rotamer: Outliers : 3.95 % Allowed : 9.11 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.75 (0.20), residues: 1665 helix: 2.33 (0.38), residues: 162 sheet: 0.74 (0.21), residues: 627 loop : 0.04 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.001 HIS A 154 PHE 0.016 0.001 PHE F 592 TYR 0.016 0.001 TYR H 117 ARG 0.007 0.001 ARG E 596 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 222 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: A 174 THR cc_start: 0.9468 (m) cc_final: 0.9118 (p) REVERT: A 267 SER cc_start: 0.7927 (OUTLIER) cc_final: 0.7260 (p) REVERT: G 10 GLU cc_start: 0.5562 (mm-30) cc_final: 0.5069 (tt0) REVERT: G 81 MET cc_start: 0.8384 (tmm) cc_final: 0.7645 (tmm) REVERT: G 106 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8187 (ttm110) REVERT: G 114 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7286 (mtmm) REVERT: E 587 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7768 (ttp-170) REVERT: H 73 ASP cc_start: 0.4568 (p0) cc_final: 0.4339 (p0) REVERT: H 78 THR cc_start: 0.7859 (m) cc_final: 0.7627 (p) REVERT: L 63 PHE cc_start: 0.6306 (m-80) cc_final: 0.6034 (m-80) REVERT: I 81 MET cc_start: 0.8134 (tmm) cc_final: 0.7838 (tmm) REVERT: I 114 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7533 (ptpt) outliers start: 56 outliers final: 35 residues processed: 253 average time/residue: 0.2600 time to fit residues: 93.9330 Evaluate side-chains 247 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 101 GLN Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 595 GLN Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 121 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13884 Z= 0.319 Angle : 0.623 6.849 18846 Z= 0.316 Chirality : 0.045 0.165 2157 Planarity : 0.004 0.047 2385 Dihedral : 6.538 52.832 2463 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.64 % Favored : 97.18 % Rotamer: Outliers : 3.95 % Allowed : 9.82 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.43 (0.20), residues: 1665 helix: 2.21 (0.38), residues: 162 sheet: 0.21 (0.20), residues: 681 loop : 0.08 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.004 0.001 HIS B 154 PHE 0.021 0.002 PHE A 132 TYR 0.018 0.002 TYR B 214 ARG 0.011 0.001 ARG D 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 212 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.8126 (OUTLIER) cc_final: 0.7439 (p) REVERT: G 81 MET cc_start: 0.8338 (tmm) cc_final: 0.8089 (tmm) REVERT: G 111 GLU cc_start: 0.8822 (pp20) cc_final: 0.8461 (pp20) REVERT: E 587 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7825 (ttp-170) REVERT: L 37 TYR cc_start: 0.5464 (m-80) cc_final: 0.4905 (m-10) REVERT: L 63 PHE cc_start: 0.6119 (m-80) cc_final: 0.5671 (m-80) REVERT: I 81 MET cc_start: 0.8144 (tmm) cc_final: 0.7811 (tmm) REVERT: I 106 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8009 (ttm110) REVERT: I 120 MET cc_start: 0.7850 (mpp) cc_final: 0.7397 (mpp) outliers start: 56 outliers final: 38 residues processed: 246 average time/residue: 0.2723 time to fit residues: 95.0879 Evaluate side-chains 242 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 101 GLN Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13884 Z= 0.169 Angle : 0.552 7.386 18846 Z= 0.278 Chirality : 0.043 0.161 2157 Planarity : 0.004 0.045 2385 Dihedral : 6.147 53.715 2463 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.52 % Favored : 97.30 % Rotamer: Outliers : 3.46 % Allowed : 11.58 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.58 (0.21), residues: 1665 helix: 2.64 (0.39), residues: 162 sheet: 0.46 (0.21), residues: 627 loop : -0.02 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 275 HIS 0.002 0.001 HIS A 154 PHE 0.020 0.001 PHE D 592 TYR 0.019 0.001 TYR B 109 ARG 0.012 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 209 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 THR cc_start: 0.9467 (m) cc_final: 0.9118 (p) REVERT: A 267 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7411 (p) REVERT: J 63 PHE cc_start: 0.6169 (m-80) cc_final: 0.5718 (m-80) REVERT: D 596 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7697 (mtt-85) REVERT: G 10 GLU cc_start: 0.5605 (mm-30) cc_final: 0.5232 (tt0) REVERT: G 81 MET cc_start: 0.8361 (tmm) cc_final: 0.8077 (tmm) REVERT: G 106 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.8147 (ttm110) REVERT: G 111 GLU cc_start: 0.8817 (pp20) cc_final: 0.8477 (pp20) REVERT: E 587 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7816 (ttp-170) REVERT: H 114 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7508 (ptpt) REVERT: C 104 TRP cc_start: 0.8872 (m100) cc_final: 0.8591 (m100) REVERT: L 37 TYR cc_start: 0.5522 (m-80) cc_final: 0.5012 (m-10) REVERT: L 63 PHE cc_start: 0.6110 (m-80) cc_final: 0.5651 (m-80) REVERT: I 81 MET cc_start: 0.8149 (tmm) cc_final: 0.7897 (tmm) REVERT: I 106 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7958 (ttm110) REVERT: I 120 MET cc_start: 0.7715 (mpp) cc_final: 0.7481 (mpp) outliers start: 49 outliers final: 30 residues processed: 241 average time/residue: 0.2821 time to fit residues: 97.4688 Evaluate side-chains 229 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 197 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain I residue 60 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13884 Z= 0.326 Angle : 0.620 7.233 18846 Z= 0.313 Chirality : 0.045 0.158 2157 Planarity : 0.004 0.045 2385 Dihedral : 6.182 59.999 2461 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 3.81 % Allowed : 11.94 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.30 (0.21), residues: 1665 helix: 2.42 (0.39), residues: 162 sheet: 0.14 (0.21), residues: 654 loop : -0.10 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.004 0.001 HIS B 154 PHE 0.021 0.002 PHE E 592 TYR 0.018 0.002 TYR L 50 ARG 0.010 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 204 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.8099 (OUTLIER) cc_final: 0.7465 (p) REVERT: J 63 PHE cc_start: 0.6244 (m-80) cc_final: 0.5741 (m-80) REVERT: G 12 LYS cc_start: 0.6744 (tptt) cc_final: 0.6468 (tppt) REVERT: G 81 MET cc_start: 0.8396 (tmm) cc_final: 0.8111 (tmm) REVERT: G 106 ARG cc_start: 0.8491 (mtp-110) cc_final: 0.8156 (ttm110) REVERT: G 111 GLU cc_start: 0.8788 (pp20) cc_final: 0.8401 (pp20) REVERT: E 587 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8041 (ttp-170) REVERT: H 114 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7520 (ptpt) REVERT: L 63 PHE cc_start: 0.6258 (m-80) cc_final: 0.5796 (m-80) REVERT: F 596 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7583 (mtt-85) REVERT: I 106 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.7964 (ttm110) outliers start: 54 outliers final: 38 residues processed: 236 average time/residue: 0.2821 time to fit residues: 93.9506 Evaluate side-chains 236 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 196 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13884 Z= 0.369 Angle : 0.644 7.438 18846 Z= 0.324 Chirality : 0.046 0.161 2157 Planarity : 0.005 0.048 2385 Dihedral : 6.138 55.142 2459 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 3.60 % Allowed : 12.85 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.21 (0.21), residues: 1665 helix: 1.60 (0.40), residues: 177 sheet: 0.19 (0.21), residues: 648 loop : -0.11 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 47 HIS 0.005 0.002 HIS A 154 PHE 0.022 0.002 PHE E 592 TYR 0.018 0.002 TYR B 214 ARG 0.010 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7494 (p) REVERT: J 63 PHE cc_start: 0.6291 (m-80) cc_final: 0.6052 (m-80) REVERT: D 578 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: G 10 GLU cc_start: 0.5819 (mm-30) cc_final: 0.5431 (tt0) REVERT: G 81 MET cc_start: 0.8429 (tmm) cc_final: 0.8126 (tmm) REVERT: G 111 GLU cc_start: 0.8844 (pp20) cc_final: 0.8474 (pp20) REVERT: G 114 LYS cc_start: 0.8419 (ttpt) cc_final: 0.7671 (ptmt) REVERT: E 587 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8088 (ttp-170) REVERT: H 48 MET cc_start: 0.7713 (ptm) cc_final: 0.7411 (ptm) REVERT: H 114 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7485 (ptpt) REVERT: L 63 PHE cc_start: 0.6255 (m-80) cc_final: 0.5831 (m-80) REVERT: I 106 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.7930 (ttm110) REVERT: I 119 TYR cc_start: 0.6262 (p90) cc_final: 0.5904 (p90) outliers start: 51 outliers final: 40 residues processed: 233 average time/residue: 0.2772 time to fit residues: 91.4134 Evaluate side-chains 240 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 7.9990 chunk 136 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13884 Z= 0.354 Angle : 0.655 12.285 18846 Z= 0.326 Chirality : 0.046 0.155 2157 Planarity : 0.005 0.044 2385 Dihedral : 6.024 50.815 2459 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.60 % Favored : 96.22 % Rotamer: Outliers : 3.25 % Allowed : 13.42 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.21), residues: 1665 helix: 1.60 (0.40), residues: 177 sheet: 0.17 (0.21), residues: 648 loop : -0.19 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.005 0.001 HIS B 154 PHE 0.020 0.002 PHE E 592 TYR 0.019 0.001 TYR B 214 ARG 0.011 0.001 ARG I 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7503 (p) REVERT: J 63 PHE cc_start: 0.6206 (m-80) cc_final: 0.5727 (m-80) REVERT: D 578 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: G 12 LYS cc_start: 0.6855 (tptt) cc_final: 0.6577 (tppt) REVERT: G 81 MET cc_start: 0.8413 (tmm) cc_final: 0.8139 (tmm) REVERT: G 111 GLU cc_start: 0.8844 (pp20) cc_final: 0.8483 (pp20) REVERT: G 120 MET cc_start: 0.7115 (mpp) cc_final: 0.6762 (mpp) REVERT: B 65 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8868 (p) REVERT: E 587 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8070 (ttp-170) REVERT: H 86 LEU cc_start: 0.5335 (mt) cc_final: 0.4913 (mp) REVERT: H 114 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7474 (ptpt) REVERT: H 119 TYR cc_start: 0.6278 (p90) cc_final: 0.6053 (p90) REVERT: H 120 MET cc_start: 0.7576 (mpp) cc_final: 0.7082 (mpp) REVERT: L 63 PHE cc_start: 0.6215 (m-80) cc_final: 0.5755 (m-80) REVERT: I 106 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7915 (ttm110) outliers start: 46 outliers final: 37 residues processed: 229 average time/residue: 0.2727 time to fit residues: 87.7793 Evaluate side-chains 240 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 548 MET Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain E residue 595 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13884 Z= 0.250 Angle : 0.598 9.314 18846 Z= 0.299 Chirality : 0.044 0.156 2157 Planarity : 0.004 0.043 2385 Dihedral : 5.830 52.070 2459 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.42 % Favored : 96.40 % Rotamer: Outliers : 2.90 % Allowed : 13.77 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.14 (0.21), residues: 1665 helix: 1.71 (0.40), residues: 180 sheet: 0.23 (0.22), residues: 624 loop : -0.28 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.003 0.001 HIS B 154 PHE 0.021 0.002 PHE E 592 TYR 0.018 0.001 TYR B 214 ARG 0.010 0.001 ARG I 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3330 Ramachandran restraints generated. 1665 Oldfield, 0 Emsley, 1665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7476 (p) REVERT: J 63 PHE cc_start: 0.6172 (m-80) cc_final: 0.5709 (m-80) REVERT: D 578 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7596 (tp30) REVERT: G 10 GLU cc_start: 0.5713 (mm-30) cc_final: 0.5386 (tt0) REVERT: G 81 MET cc_start: 0.8367 (tmm) cc_final: 0.8078 (tmm) REVERT: G 111 GLU cc_start: 0.8798 (pp20) cc_final: 0.8438 (pp20) REVERT: G 120 MET cc_start: 0.7150 (mpp) cc_final: 0.6812 (mpp) REVERT: B 65 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8836 (p) REVERT: E 587 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.8038 (ttp-170) REVERT: H 114 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7434 (ptpt) REVERT: H 119 TYR cc_start: 0.6356 (p90) cc_final: 0.6136 (p90) REVERT: H 120 MET cc_start: 0.7625 (mpp) cc_final: 0.7209 (mpp) REVERT: L 63 PHE cc_start: 0.6258 (m-80) cc_final: 0.5855 (m-80) REVERT: F 596 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7835 (mtt-85) REVERT: I 106 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7803 (ttm110) REVERT: I 119 TYR cc_start: 0.6308 (p90) cc_final: 0.6014 (p90) outliers start: 41 outliers final: 36 residues processed: 230 average time/residue: 0.2674 time to fit residues: 87.3515 Evaluate side-chains 245 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 205 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 71 ASP Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain D residue 578 GLU Chi-restraints excluded: chain D residue 581 THR Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 267 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain E residue 520 THR Chi-restraints excluded: chain E residue 587 ARG Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 109 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092223 restraints weight = 22388.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.094670 restraints weight = 16826.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.095366 restraints weight = 12791.799| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13884 Z= 0.316 Angle : 0.636 12.063 18846 Z= 0.316 Chirality : 0.045 0.155 2157 Planarity : 0.004 0.044 2385 Dihedral : 5.822 52.447 2459 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.26 % Favored : 95.56 % Rotamer: Outliers : 3.11 % Allowed : 13.70 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.20 (0.21), residues: 1665 helix: 1.76 (0.40), residues: 177 sheet: 0.25 (0.21), residues: 639 loop : -0.22 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 104 HIS 0.004 0.001 HIS A 154 PHE 0.021 0.002 PHE E 592 TYR 0.020 0.001 TYR B 214 ARG 0.010 0.001 ARG I 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.80 seconds wall clock time: 50 minutes 55.42 seconds (3055.42 seconds total)