Starting phenix.real_space_refine on Tue Feb 20 06:01:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wg7_32479/02_2024/7wg7_32479.pdb" } resolution = 4.0 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= 0.002 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 118 5.16 5 C 17235 2.51 5 N 4408 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27041 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 58, 'TRANS': 1039} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1038} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8770 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1057} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "K" 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" 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: "T" 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.72, per 1000 atoms: 0.51 Number of scatterers: 27041 At special positions: 0 Unit cell: (146.59, 147.66, 216.14, 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 118 16.00 O 5280 8.00 N 4408 7.00 C 17235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 125 " " NAG B1303 " - " ASN B 17 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 145 " " NAG C1303 " - " ASN C 17 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 717 " " NAG C1311 " - " ASN C 709 " " NAG D 1 " - " ASN B 233 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN A 233 " " NAG L 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG Q 1 " - " ASN C 233 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.44 Conformation dependent library (CDL) restraints added in 4.8 seconds 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6230 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 40 sheets defined 23.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.767A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.141A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.129A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.695A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.509A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.030A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.586A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.709A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.708A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.822A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.673A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.598A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.147A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.573A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.506A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1157 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.948A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.807A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.540A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.556A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.723A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.509A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.938A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.751A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.398A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.544A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.024A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 4.232A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.669A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 616 through 623 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.525A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.703A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 849 through 854 removed outlier: 4.127A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.631A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.807A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.814A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.750A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.869A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.859A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.463A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.313A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'C' and resid 1145 through 1161 removed outlier: 4.223A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.581A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 185 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 186 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.517A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.965A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.697A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.884A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.026A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.542A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.734A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 186 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.664A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.841A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A 132 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.424A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.540A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.800A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.185A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.189A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.617A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.199A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.239A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.338A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.502A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.941A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.531A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2493 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: 11.01 Time building geometry restraints manager: 11.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8490 1.35 - 1.47: 7101 1.47 - 1.59: 11919 1.59 - 1.72: 0 1.72 - 1.84: 148 Bond restraints: 27658 Sorted by residual: bond pdb=" C LEU A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.12e-02 7.97e+03 3.64e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 27653 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.85: 608 105.85 - 113.59: 15446 113.59 - 121.34: 14131 121.34 - 129.09: 7306 129.09 - 136.84: 121 Bond angle restraints: 37612 Sorted by residual: angle pdb=" N PRO A 942 " pdb=" CA PRO A 942 " pdb=" CB PRO A 942 " ideal model delta sigma weight residual 101.83 110.19 -8.36 8.40e-01 1.42e+00 9.92e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 101.83 110.16 -8.33 8.40e-01 1.42e+00 9.84e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.36 110.26 -6.90 8.80e-01 1.29e+00 6.15e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.33 110.53 -7.20 9.30e-01 1.16e+00 6.00e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 111.77 103.78 7.99 1.04e+00 9.25e-01 5.91e+01 ... (remaining 37607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.11: 16138 25.11 - 50.22: 990 50.22 - 75.33: 156 75.33 - 100.43: 83 100.43 - 125.54: 77 Dihedral angle restraints: 17444 sinusoidal: 7771 harmonic: 9673 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.50 -87.50 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.22 83.78 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA THR B1117 " pdb=" C THR B1117 " pdb=" N ASP B1118 " pdb=" CA ASP B1118 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 17441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4228 0.116 - 0.232: 189 0.232 - 0.347: 25 0.347 - 0.463: 2 0.463 - 0.579: 3 Chirality restraints: 4447 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 4444 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A1143 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 997 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ILE B 997 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 997 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 998 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 998 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR B 998 " 0.048 2.00e-02 2.50e+03 pdb=" O THR B 998 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 999 " -0.016 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4799 2.77 - 3.30: 25154 3.30 - 3.83: 43886 3.83 - 4.37: 47418 4.37 - 4.90: 81899 Nonbonded interactions: 203156 Sorted by model distance: nonbonded pdb=" OD1 ASN A 354 " pdb=" OG SER A 399 " model vdw 2.237 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.245 2.440 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.261 2.440 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.268 2.440 ... (remaining 203151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 702 or resid 704 through 1162 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 14 through 702 or resid 704 through 1162 or resid 1301 thr \ ough 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 849 through 1162 or resid 1301 thr \ ough 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'U' selection = chain 'V' } 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.310 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 69.220 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.005 0.107 27658 Z= 0.324 Angle : 0.879 13.835 37612 Z= 0.458 Chirality : 0.059 0.579 4447 Planarity : 0.006 0.094 4756 Dihedral : 19.046 125.542 11097 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.14), residues: 3283 helix: -0.18 (0.19), residues: 671 sheet: -0.17 (0.21), residues: 578 loop : -2.34 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.017 0.001 HIS B 625 PHE 0.027 0.001 PHE B 106 TYR 0.018 0.001 TYR C1067 ARG 0.011 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 3.157 Fit side-chains revert: symmetry clash REVERT: B 87 ASN cc_start: 0.4302 (OUTLIER) cc_final: 0.3625 (p0) REVERT: B 636 TYR cc_start: 0.5742 (t80) cc_final: 0.5472 (m-80) REVERT: A 167 TYR cc_start: 0.8242 (t80) cc_final: 0.7982 (t80) REVERT: C 613 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: C 896 ILE cc_start: 0.8178 (mm) cc_final: 0.7927 (tp) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.3336 time to fit residues: 84.6339 Evaluate side-chains 100 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 613 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 257 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1011 GLN B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 27658 Z= 0.396 Angle : 0.790 12.331 37612 Z= 0.390 Chirality : 0.051 0.452 4447 Planarity : 0.005 0.077 4756 Dihedral : 16.342 115.830 5086 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 1.00 % Allowed : 10.71 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.93 (0.14), residues: 3283 helix: 0.41 (0.20), residues: 682 sheet: -0.48 (0.21), residues: 601 loop : -2.28 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 633 HIS 0.006 0.001 HIS B1058 PHE 0.027 0.002 PHE A 759 TYR 0.029 0.002 TYR C1067 ARG 0.010 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 2.890 Fit side-chains revert: symmetry clash REVERT: B 174 MET cc_start: 0.5791 (mtm) cc_final: 0.5571 (mtm) REVERT: A 636 TYR cc_start: 0.7937 (t80) cc_final: 0.7581 (t80) REVERT: A 731 MET cc_start: 0.8684 (ppp) cc_final: 0.8232 (ppp) REVERT: C 409 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7653 (mm110) REVERT: C 613 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8211 (pp30) REVERT: C 1031 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7489 (mt-10) outliers start: 29 outliers final: 18 residues processed: 118 average time/residue: 0.3225 time to fit residues: 66.9988 Evaluate side-chains 112 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 323 optimal weight: 0.6980 chunk 266 optimal weight: 5.9990 chunk 296 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27658 Z= 0.219 Angle : 0.665 11.412 37612 Z= 0.323 Chirality : 0.048 0.411 4447 Planarity : 0.004 0.076 4756 Dihedral : 14.520 114.876 5084 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.07 % Allowed : 14.98 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.66 (0.14), residues: 3283 helix: 0.92 (0.21), residues: 671 sheet: -0.32 (0.22), residues: 570 loop : -2.18 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.004 0.001 HIS B 204 PHE 0.019 0.001 PHE A 759 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 3.133 Fit side-chains revert: symmetry clash REVERT: B 902 MET cc_start: 0.9111 (tpp) cc_final: 0.8907 (tpp) REVERT: A 636 TYR cc_start: 0.7846 (t80) cc_final: 0.7525 (t80) REVERT: A 643 PHE cc_start: 0.7394 (m-80) cc_final: 0.6996 (m-80) REVERT: A 882 ILE cc_start: 0.9155 (tp) cc_final: 0.8905 (mt) REVERT: C 613 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8270 (pp30) REVERT: C 1031 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7442 (mt-10) outliers start: 31 outliers final: 19 residues processed: 128 average time/residue: 0.3298 time to fit residues: 74.4607 Evaluate side-chains 120 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 6.9990 chunk 225 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27658 Z= 0.182 Angle : 0.634 11.414 37612 Z= 0.305 Chirality : 0.047 0.404 4447 Planarity : 0.004 0.074 4756 Dihedral : 12.894 113.433 5084 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.79 % Allowed : 16.70 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.15), residues: 3283 helix: 1.17 (0.21), residues: 670 sheet: -0.23 (0.21), residues: 609 loop : -2.14 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.003 0.001 HIS B 204 PHE 0.020 0.001 PHE A 759 TYR 0.016 0.001 TYR C1067 ARG 0.005 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 110 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8682 (tpp) cc_final: 0.8291 (tpt) REVERT: A 511 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8321 (t) REVERT: A 636 TYR cc_start: 0.7766 (t80) cc_final: 0.7419 (t80) REVERT: A 882 ILE cc_start: 0.9132 (tp) cc_final: 0.8885 (mt) REVERT: C 128 ILE cc_start: 0.8886 (mm) cc_final: 0.8460 (tp) REVERT: C 613 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8192 (pp30) REVERT: C 1031 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7366 (mt-10) outliers start: 52 outliers final: 32 residues processed: 150 average time/residue: 0.3206 time to fit residues: 84.6473 Evaluate side-chains 131 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 97 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 271 optimal weight: 7.9990 chunk 219 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 27658 Z= 0.417 Angle : 0.793 10.270 37612 Z= 0.394 Chirality : 0.050 0.404 4447 Planarity : 0.005 0.072 4756 Dihedral : 12.863 117.649 5084 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 3.20 % Allowed : 18.39 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3283 helix: 0.57 (0.20), residues: 678 sheet: -0.66 (0.21), residues: 591 loop : -2.36 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 64 HIS 0.008 0.001 HIS B1058 PHE 0.032 0.002 PHE A 759 TYR 0.029 0.002 TYR C1067 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 95 time to evaluate : 3.102 Fit side-chains revert: symmetry clash REVERT: A 167 TYR cc_start: 0.8121 (t80) cc_final: 0.7916 (t80) REVERT: A 461 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6132 (tp) REVERT: A 495 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.4539 (m-10) REVERT: A 511 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8212 (t) REVERT: A 636 TYR cc_start: 0.7921 (t80) cc_final: 0.7550 (t80) REVERT: A 882 ILE cc_start: 0.9235 (tp) cc_final: 0.8975 (mt) REVERT: C 583 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7255 (pm20) REVERT: C 613 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8403 (pp30) REVERT: C 867 ASP cc_start: 0.7819 (p0) cc_final: 0.7576 (p0) REVERT: C 1031 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7585 (mt-10) REVERT: C 1145 LEU cc_start: 0.4968 (OUTLIER) cc_final: 0.3981 (tp) outliers start: 93 outliers final: 56 residues processed: 178 average time/residue: 0.3275 time to fit residues: 102.4260 Evaluate side-chains 151 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 89 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 0.9980 chunk 286 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 264 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN C 134 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27658 Z= 0.214 Angle : 0.662 11.008 37612 Z= 0.324 Chirality : 0.048 0.400 4447 Planarity : 0.004 0.072 4756 Dihedral : 12.164 115.144 5084 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.48 % Allowed : 20.08 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 3283 helix: 1.08 (0.21), residues: 670 sheet: -0.49 (0.21), residues: 596 loop : -2.22 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.004 0.001 HIS C1083 PHE 0.027 0.001 PHE A 219 TYR 0.016 0.001 TYR A 167 ARG 0.006 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 96 time to evaluate : 2.717 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8648 (tpp) cc_final: 0.8410 (tpp) REVERT: A 495 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.4539 (m-10) REVERT: A 511 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8207 (t) REVERT: A 636 TYR cc_start: 0.7902 (t80) cc_final: 0.7427 (t80) REVERT: A 731 MET cc_start: 0.8703 (ppp) cc_final: 0.8222 (ppp) REVERT: A 882 ILE cc_start: 0.9226 (tp) cc_final: 0.8968 (mt) REVERT: C 433 VAL cc_start: -0.0184 (OUTLIER) cc_final: -0.0436 (t) REVERT: C 613 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8388 (pp30) REVERT: C 867 ASP cc_start: 0.7665 (p0) cc_final: 0.7408 (p0) REVERT: C 1031 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7341 (mt-10) REVERT: C 1145 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.3961 (tp) outliers start: 72 outliers final: 41 residues processed: 160 average time/residue: 0.3385 time to fit residues: 95.5222 Evaluate side-chains 137 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 91 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 27658 Z= 0.374 Angle : 0.750 11.193 37612 Z= 0.372 Chirality : 0.049 0.403 4447 Planarity : 0.004 0.069 4756 Dihedral : 12.109 116.557 5084 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 3.31 % Allowed : 20.49 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3283 helix: 0.77 (0.20), residues: 681 sheet: -0.72 (0.21), residues: 606 loop : -2.38 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 PHE 0.028 0.002 PHE A 759 TYR 0.027 0.002 TYR C1067 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 90 time to evaluate : 3.098 Fit side-chains revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9127 (t0) cc_final: 0.8790 (t70) REVERT: A 461 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6198 (tp) REVERT: A 495 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.4524 (m-10) REVERT: A 511 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8206 (t) REVERT: A 636 TYR cc_start: 0.7890 (t80) cc_final: 0.7524 (t80) REVERT: A 909 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7577 (tp) REVERT: C 409 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7705 (mm110) REVERT: C 433 VAL cc_start: -0.0085 (OUTLIER) cc_final: -0.0381 (t) REVERT: C 583 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7264 (pm20) REVERT: C 613 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8489 (pp30) REVERT: C 867 ASP cc_start: 0.7873 (p0) cc_final: 0.7593 (p0) REVERT: C 1031 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 1145 LEU cc_start: 0.4862 (OUTLIER) cc_final: 0.3926 (tp) outliers start: 96 outliers final: 67 residues processed: 178 average time/residue: 0.3182 time to fit residues: 99.3480 Evaluate side-chains 163 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 87 time to evaluate : 4.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 189 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 27658 Z= 0.276 Angle : 0.696 11.149 37612 Z= 0.343 Chirality : 0.048 0.397 4447 Planarity : 0.004 0.068 4756 Dihedral : 11.693 115.986 5084 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.96 % Allowed : 21.28 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.87 (0.14), residues: 3283 helix: 0.91 (0.21), residues: 683 sheet: -0.67 (0.21), residues: 602 loop : -2.35 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.005 0.001 HIS C1083 PHE 0.022 0.001 PHE A 759 TYR 0.020 0.001 TYR C1067 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 91 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 428 ASP cc_start: 0.9135 (t0) cc_final: 0.8795 (t70) REVERT: A 461 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6185 (tp) REVERT: A 495 TYR cc_start: 0.6782 (OUTLIER) cc_final: 0.4609 (m-10) REVERT: A 511 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8170 (t) REVERT: A 636 TYR cc_start: 0.7877 (t80) cc_final: 0.7542 (t80) REVERT: A 882 ILE cc_start: 0.9158 (tp) cc_final: 0.8921 (mt) REVERT: C 84 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6927 (tt) REVERT: C 433 VAL cc_start: -0.0096 (OUTLIER) cc_final: -0.0397 (t) REVERT: C 613 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8533 (pp30) REVERT: C 867 ASP cc_start: 0.7890 (p0) cc_final: 0.7591 (p0) REVERT: C 1031 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7406 (mt-10) REVERT: C 1145 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.3981 (tp) outliers start: 86 outliers final: 67 residues processed: 167 average time/residue: 0.3241 time to fit residues: 94.8344 Evaluate side-chains 163 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 89 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 277 optimal weight: 6.9990 chunk 295 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 294 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27658 Z= 0.168 Angle : 0.636 11.560 37612 Z= 0.311 Chirality : 0.047 0.414 4447 Planarity : 0.004 0.070 4756 Dihedral : 11.031 113.382 5084 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.20 % Allowed : 22.28 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.54 (0.15), residues: 3283 helix: 1.38 (0.21), residues: 666 sheet: -0.37 (0.22), residues: 580 loop : -2.20 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE A 219 TYR 0.012 0.001 TYR C1067 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 98 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8589 (tpp) cc_final: 0.8276 (tpp) REVERT: A 167 TYR cc_start: 0.8132 (t80) cc_final: 0.7902 (t80) REVERT: A 428 ASP cc_start: 0.9098 (t0) cc_final: 0.8703 (t70) REVERT: A 636 TYR cc_start: 0.7821 (t80) cc_final: 0.7382 (t80) REVERT: A 731 MET cc_start: 0.8743 (ppp) cc_final: 0.8220 (ppp) REVERT: A 882 ILE cc_start: 0.9143 (tp) cc_final: 0.8939 (mt) REVERT: C 433 VAL cc_start: -0.0009 (OUTLIER) cc_final: -0.0257 (t) REVERT: C 583 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: C 867 ASP cc_start: 0.7764 (p0) cc_final: 0.7432 (p0) REVERT: C 1145 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.3831 (tp) outliers start: 64 outliers final: 45 residues processed: 152 average time/residue: 0.3666 time to fit residues: 97.6155 Evaluate side-chains 140 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 92 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 148 optimal weight: 0.7980 chunk 217 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 301 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27658 Z= 0.175 Angle : 0.633 11.974 37612 Z= 0.310 Chirality : 0.047 0.413 4447 Planarity : 0.004 0.071 4756 Dihedral : 10.646 113.379 5081 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 1.96 % Allowed : 22.49 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.48 (0.15), residues: 3283 helix: 1.36 (0.21), residues: 668 sheet: -0.31 (0.22), residues: 585 loop : -2.15 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 PHE 0.024 0.001 PHE A 759 TYR 0.019 0.001 TYR B 636 ARG 0.008 0.000 ARG C 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 97 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8551 (tpp) cc_final: 0.8279 (tpp) REVERT: A 167 TYR cc_start: 0.8109 (t80) cc_final: 0.7877 (t80) REVERT: A 428 ASP cc_start: 0.9114 (t0) cc_final: 0.8713 (t70) REVERT: A 461 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6251 (tp) REVERT: A 636 TYR cc_start: 0.7842 (t80) cc_final: 0.7434 (t80) REVERT: A 731 MET cc_start: 0.8723 (ppp) cc_final: 0.8222 (ppp) REVERT: A 882 ILE cc_start: 0.9150 (tp) cc_final: 0.8930 (mt) REVERT: C 433 VAL cc_start: -0.0027 (OUTLIER) cc_final: -0.0261 (t) REVERT: C 565 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: C 583 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: C 763 LEU cc_start: 0.9225 (mt) cc_final: 0.8997 (pp) REVERT: C 867 ASP cc_start: 0.7752 (p0) cc_final: 0.7422 (p0) REVERT: C 1145 LEU cc_start: 0.4615 (OUTLIER) cc_final: 0.3890 (tp) outliers start: 57 outliers final: 47 residues processed: 144 average time/residue: 0.3410 time to fit residues: 85.1762 Evaluate side-chains 142 residues out of total 2913 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 90 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 901 GLN Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 952 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 207 optimal weight: 0.5980 chunk 278 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 268 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 48 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: B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.113190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.084434 restraints weight = 93539.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.085980 restraints weight = 68935.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085281 restraints weight = 52191.188| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.153 27658 Z= 0.222 Angle : 0.756 59.194 37612 Z= 0.398 Chirality : 0.048 0.651 4447 Planarity : 0.004 0.071 4756 Dihedral : 10.645 113.332 5081 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.13 % Allowed : 22.42 % Favored : 75.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.15), residues: 3283 helix: 1.36 (0.21), residues: 668 sheet: -0.30 (0.22), residues: 580 loop : -2.16 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.002 0.001 HIS A1083 PHE 0.022 0.001 PHE A 759 TYR 0.025 0.001 TYR A 873 ARG 0.007 0.000 ARG C 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.70 seconds wall clock time: 75 minutes 22.08 seconds (4522.08 seconds total)