Starting phenix.real_space_refine on Sun Feb 18 06:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0s_11970/02_2024/7b0s_11970_updated.pdb" } resolution = 3.6 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= 0.001 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: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 P 4 5.49 5 S 108 5.16 5 Cl 4 4.86 5 C 13766 2.51 5 N 3452 2.21 5 O 3726 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A GLU 469": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A GLU 732": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ASP 741": "OD1" <-> "OD2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 545": "OE1" <-> "OE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 707": "OE1" <-> "OE2" Residue "B ARG 710": "NH1" <-> "NH2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ASP 741": "OD1" <-> "OD2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 469": "OE1" <-> "OE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 629": "OD1" <-> "OD2" Residue "C TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 707": "OE1" <-> "OE2" Residue "C ARG 710": "NH1" <-> "NH2" Residue "C GLU 732": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ASP 741": "OD1" <-> "OD2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D GLU 84": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 545": "OE1" <-> "OE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 629": "OD1" <-> "OD2" Residue "D TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 707": "OE1" <-> "OE2" Residue "D ARG 710": "NH1" <-> "NH2" Residue "D GLU 732": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ASP 741": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21076 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5215 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 5219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5219 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 6 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 51 Unusual residues: {' CA': 1, '44E': 1, 'S9Q': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.85, per 1000 atoms: 0.51 Number of scatterers: 21076 At special positions: 0 Unit cell: (139.23, 139.23, 137.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 4 19.99 Cl 4 17.00 S 108 16.00 P 4 15.00 F 12 9.00 O 3726 8.00 N 3452 7.00 C 13766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 3.4 seconds 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 124 helices and 0 sheets defined 65.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.919A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.624A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 216 through 233 removed outlier: 4.075A pdb=" N LYS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 258 removed outlier: 3.919A pdb=" N HIS A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 330 through 349 removed outlier: 3.690A pdb=" N VAL A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 362 through 384 removed outlier: 3.730A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 Proline residue: A 408 - end of helix removed outlier: 4.663A pdb=" N ASP A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 removed outlier: 3.662A pdb=" N MET A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 457 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 473 through 498 removed outlier: 3.551A pdb=" N VAL A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 517 removed outlier: 4.067A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 538 removed outlier: 4.477A pdb=" N CYS A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A 525 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 526 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 591 through 611 Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.662A pdb=" N MET A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.829A pdb=" N SER A 645 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 720 Processing helix chain 'A' and resid 732 through 752 removed outlier: 4.108A pdb=" N GLU A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 742 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.918A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 155 through 164 removed outlier: 3.624A pdb=" N GLN B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 203 Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 216 through 233 removed outlier: 4.075A pdb=" N LYS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 258 removed outlier: 3.919A pdb=" N HIS B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 301 No H-bonds generated for 'chain 'B' and resid 298 through 301' Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 330 through 349 removed outlier: 3.690A pdb=" N VAL B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 362 through 384 removed outlier: 3.731A pdb=" N ILE B 367 " --> pdb=" O PHE B 363 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 424 Proline residue: B 408 - end of helix removed outlier: 4.663A pdb=" N ASP B 423 " --> pdb=" O LYS B 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 removed outlier: 3.662A pdb=" N MET B 437 " --> pdb=" O TRP B 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 467 No H-bonds generated for 'chain 'B' and resid 465 through 467' Processing helix chain 'B' and resid 473 through 498 removed outlier: 3.551A pdb=" N VAL B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA B 498 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 517 removed outlier: 4.067A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 538 removed outlier: 4.476A pdb=" N CYS B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 525 " --> pdb=" O PHE B 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 573 Processing helix chain 'B' and resid 591 through 611 Processing helix chain 'B' and resid 614 through 627 removed outlier: 3.662A pdb=" N MET B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS B 626 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 646 removed outlier: 3.829A pdb=" N SER B 645 " --> pdb=" O LYS B 641 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 720 Processing helix chain 'B' and resid 732 through 752 removed outlier: 4.108A pdb=" N GLU B 737 " --> pdb=" O GLU B 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 46 through 58 removed outlier: 3.919A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 155 through 164 removed outlier: 3.624A pdb=" N GLN C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS C 164 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 216 through 233 removed outlier: 4.075A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 258 removed outlier: 3.919A pdb=" N HIS C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 298 through 301 No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 330 through 349 removed outlier: 3.690A pdb=" N VAL C 334 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE C 340 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.730A pdb=" N ILE C 367 " --> pdb=" O PHE C 363 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 424 Proline residue: C 408 - end of helix removed outlier: 4.663A pdb=" N ASP C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 removed outlier: 3.662A pdb=" N MET C 437 " --> pdb=" O TRP C 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 467 No H-bonds generated for 'chain 'C' and resid 465 through 467' Processing helix chain 'C' and resid 473 through 498 removed outlier: 3.551A pdb=" N VAL C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA C 498 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 517 removed outlier: 4.067A pdb=" N LEU C 513 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 538 removed outlier: 4.476A pdb=" N CYS C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU C 525 " --> pdb=" O PHE C 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 526 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 Processing helix chain 'C' and resid 591 through 611 Processing helix chain 'C' and resid 614 through 627 removed outlier: 3.662A pdb=" N MET C 619 " --> pdb=" O MET C 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 646 removed outlier: 3.829A pdb=" N SER C 645 " --> pdb=" O LYS C 641 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 720 Processing helix chain 'C' and resid 732 through 752 removed outlier: 4.108A pdb=" N GLU C 737 " --> pdb=" O GLU C 733 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 46 through 58 removed outlier: 3.918A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 155 through 164 removed outlier: 3.624A pdb=" N GLN D 163 " --> pdb=" O LYS D 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS D 164 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 216 through 233 removed outlier: 4.075A pdb=" N LYS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 258 removed outlier: 3.919A pdb=" N HIS D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 256 " --> pdb=" O ALA D 252 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 298 through 301 No H-bonds generated for 'chain 'D' and resid 298 through 301' Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 330 through 349 removed outlier: 3.690A pdb=" N VAL D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Proline residue: D 341 - end of helix Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 362 through 384 removed outlier: 3.730A pdb=" N ILE D 367 " --> pdb=" O PHE D 363 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 Proline residue: D 408 - end of helix removed outlier: 4.663A pdb=" N ASP D 423 " --> pdb=" O LYS D 419 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY D 424 " --> pdb=" O GLN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 removed outlier: 3.661A pdb=" N MET D 437 " --> pdb=" O TRP D 433 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 457 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 458 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 498 removed outlier: 3.551A pdb=" N VAL D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 481 " --> pdb=" O ALA D 477 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER D 494 " --> pdb=" O LEU D 490 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N PHE D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ALA D 498 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 517 removed outlier: 4.067A pdb=" N LEU D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE D 516 " --> pdb=" O MET D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 538 removed outlier: 4.476A pdb=" N CYS D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU D 525 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 526 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 Processing helix chain 'D' and resid 591 through 611 Processing helix chain 'D' and resid 614 through 627 removed outlier: 3.662A pdb=" N MET D 619 " --> pdb=" O MET D 615 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS D 626 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 646 removed outlier: 3.829A pdb=" N SER D 645 " --> pdb=" O LYS D 641 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 702 through 720 Processing helix chain 'D' and resid 732 through 752 removed outlier: 4.108A pdb=" N GLU D 737 " --> pdb=" O GLU D 733 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 3012 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: 5.93 Time building geometry restraints manager: 9.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3314 1.30 - 1.43: 5916 1.43 - 1.55: 12162 1.55 - 1.68: 4 1.68 - 1.80: 180 Bond restraints: 21576 Sorted by residual: bond pdb=" C6 S9Q B1001 " pdb=" N3 S9Q B1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q C1001 " pdb=" N3 S9Q C1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q A1001 " pdb=" N3 S9Q A1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" C6 S9Q D1001 " pdb=" N3 S9Q D1001 " ideal model delta sigma weight residual 1.287 1.478 -0.191 2.00e-02 2.50e+03 9.15e+01 bond pdb=" N2 S9Q D1001 " pdb=" N3 S9Q D1001 " ideal model delta sigma weight residual 1.317 1.466 -0.149 2.00e-02 2.50e+03 5.57e+01 ... (remaining 21571 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.71: 523 106.71 - 113.58: 12202 113.58 - 120.45: 8926 120.45 - 127.32: 7328 127.32 - 134.19: 256 Bond angle restraints: 29235 Sorted by residual: angle pdb=" C1 S9Q D1001 " pdb=" N4 S9Q D1001 " pdb=" C8 S9Q D1001 " ideal model delta sigma weight residual 124.28 113.92 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C1 S9Q A1001 " pdb=" N4 S9Q A1001 " pdb=" C8 S9Q A1001 " ideal model delta sigma weight residual 124.28 113.92 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C1 S9Q C1001 " pdb=" N4 S9Q C1001 " pdb=" C8 S9Q C1001 " ideal model delta sigma weight residual 124.28 113.92 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C1 S9Q B1001 " pdb=" N4 S9Q B1001 " pdb=" C8 S9Q B1001 " ideal model delta sigma weight residual 124.28 113.92 10.36 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N ILE D 359 " pdb=" CA ILE D 359 " pdb=" C ILE D 359 " ideal model delta sigma weight residual 111.81 108.93 2.88 8.60e-01 1.35e+00 1.12e+01 ... (remaining 29230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.75: 11862 24.75 - 49.51: 799 49.51 - 74.26: 108 74.26 - 99.01: 20 99.01 - 123.77: 4 Dihedral angle restraints: 12793 sinusoidal: 5197 harmonic: 7596 Sorted by residual: dihedral pdb=" C10 S9Q A1001 " pdb=" C9 S9Q A1001 " pdb=" N4 S9Q A1001 " pdb=" C8 S9Q A1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C10 S9Q B1001 " pdb=" C9 S9Q B1001 " pdb=" N4 S9Q B1001 " pdb=" C8 S9Q B1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C10 S9Q D1001 " pdb=" C9 S9Q D1001 " pdb=" N4 S9Q D1001 " pdb=" C8 S9Q D1001 " ideal model delta sinusoidal sigma weight residual -92.34 31.43 -123.77 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 12790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1750 0.033 - 0.065: 1066 0.065 - 0.097: 363 0.097 - 0.130: 85 0.130 - 0.162: 12 Chirality restraints: 3276 Sorted by residual: chirality pdb=" CA PRO B 304 " pdb=" N PRO B 304 " pdb=" C PRO B 304 " pdb=" CB PRO B 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO C 304 " pdb=" N PRO C 304 " pdb=" C PRO C 304 " pdb=" CB PRO C 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO A 304 " pdb=" N PRO A 304 " pdb=" C PRO A 304 " pdb=" CB PRO A 304 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 3273 not shown) Planarity restraints: 3619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 67 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 68 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 68 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 67 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO D 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO D 68 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 68 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 67 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO C 68 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 68 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 68 " 0.025 5.00e-02 4.00e+02 ... (remaining 3616 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4031 2.75 - 3.29: 21069 3.29 - 3.83: 33258 3.83 - 4.36: 37336 4.36 - 4.90: 64224 Nonbonded interactions: 159918 Sorted by model distance: nonbonded pdb=" OE2 GLU D 417 " pdb=" OH TYR D 429 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU A 417 " pdb=" OH TYR A 429 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU C 417 " pdb=" OH TYR C 429 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU B 417 " pdb=" OH TYR B 429 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR A 523 " pdb=" OH TYR A 604 " model vdw 2.265 2.440 ... (remaining 159913 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 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 754 or resid 1001 through 1003)) selection = (chain 'B' and (resid 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 754 or resid 1001 through 1003)) selection = chain 'C' selection = (chain 'D' and (resid 29 through 55 or (resid 56 and (name N or name CA or name \ C or name O or name CB )) or resid 57 through 754 or resid 1001 through 1003)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.030 Extract box with map and model: 6.080 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 54.000 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.120 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.009 0.191 21576 Z= 0.604 Angle : 0.772 10.360 29235 Z= 0.401 Chirality : 0.045 0.162 3276 Planarity : 0.004 0.045 3619 Dihedral : 16.129 123.766 7849 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.35 % Allowed : 0.18 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2516 helix: 0.24 (0.13), residues: 1800 sheet: None (None), residues: 0 loop : -1.72 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 409 HIS 0.002 0.001 HIS A 630 PHE 0.017 0.002 PHE B 300 TYR 0.018 0.002 TYR B 624 ARG 0.004 0.001 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 222 time to evaluate : 2.422 Fit side-chains REVERT: A 335 PHE cc_start: 0.8202 (t80) cc_final: 0.7891 (t80) REVERT: A 421 MET cc_start: 0.8136 (tmm) cc_final: 0.7681 (tmm) REVERT: A 437 MET cc_start: 0.7770 (mtp) cc_final: 0.7508 (mtm) REVERT: A 441 MET cc_start: 0.8379 (mtm) cc_final: 0.7810 (mtp) REVERT: B 335 PHE cc_start: 0.8202 (t80) cc_final: 0.7892 (t80) REVERT: B 421 MET cc_start: 0.8127 (tmm) cc_final: 0.7670 (tmm) REVERT: B 437 MET cc_start: 0.7760 (mtp) cc_final: 0.7500 (mtm) REVERT: B 441 MET cc_start: 0.8388 (mtm) cc_final: 0.7808 (mtp) REVERT: C 335 PHE cc_start: 0.8201 (t80) cc_final: 0.7891 (t80) REVERT: C 421 MET cc_start: 0.8135 (tmm) cc_final: 0.7684 (tmm) REVERT: C 437 MET cc_start: 0.7752 (mtp) cc_final: 0.7498 (mtm) REVERT: C 441 MET cc_start: 0.8388 (mtm) cc_final: 0.7812 (mtp) REVERT: D 335 PHE cc_start: 0.8208 (t80) cc_final: 0.7898 (t80) REVERT: D 421 MET cc_start: 0.8135 (tmm) cc_final: 0.7673 (tmm) REVERT: D 437 MET cc_start: 0.7761 (mtp) cc_final: 0.7503 (mtm) REVERT: D 441 MET cc_start: 0.8372 (mtm) cc_final: 0.7809 (mtp) outliers start: 8 outliers final: 4 residues processed: 226 average time/residue: 0.3051 time to fit residues: 110.2377 Evaluate side-chains 185 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 GLN Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain D residue 420 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 395 GLN A 420 GLN A 442 ASN B 80 ASN B 395 GLN B 442 ASN C 80 ASN C 395 GLN C 420 GLN C 442 ASN D 80 ASN D 395 GLN D 420 GLN D 442 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21576 Z= 0.132 Angle : 0.482 6.348 29235 Z= 0.244 Chirality : 0.036 0.134 3276 Planarity : 0.004 0.048 3619 Dihedral : 8.864 111.190 2908 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.57 % Allowed : 6.45 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2516 helix: 0.99 (0.13), residues: 1772 sheet: None (None), residues: 0 loop : -1.50 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.004 0.000 HIS A 192 PHE 0.010 0.001 PHE A 92 TYR 0.010 0.001 TYR D 582 ARG 0.003 0.000 ARG D 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 236 time to evaluate : 2.369 Fit side-chains REVERT: A 421 MET cc_start: 0.8035 (tmm) cc_final: 0.7551 (tmm) REVERT: A 441 MET cc_start: 0.8333 (mtm) cc_final: 0.7620 (mtp) REVERT: B 421 MET cc_start: 0.8048 (tmm) cc_final: 0.7580 (tmm) REVERT: B 441 MET cc_start: 0.8338 (mtm) cc_final: 0.7627 (mtp) REVERT: B 753 MET cc_start: 0.7786 (mtp) cc_final: 0.7180 (mmm) REVERT: C 421 MET cc_start: 0.8042 (tmm) cc_final: 0.7566 (tmm) REVERT: C 441 MET cc_start: 0.8342 (mtm) cc_final: 0.7632 (mtp) REVERT: C 753 MET cc_start: 0.7763 (mtp) cc_final: 0.7347 (mmt) REVERT: D 421 MET cc_start: 0.8037 (tmm) cc_final: 0.7554 (tmm) REVERT: D 441 MET cc_start: 0.8324 (mtm) cc_final: 0.7630 (mtp) outliers start: 13 outliers final: 13 residues processed: 241 average time/residue: 0.3224 time to fit residues: 121.3854 Evaluate side-chains 215 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 193 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 230 optimal weight: 0.0030 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN B 64 ASN B 420 GLN D 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21576 Z= 0.239 Angle : 0.503 6.315 29235 Z= 0.254 Chirality : 0.037 0.133 3276 Planarity : 0.004 0.047 3619 Dihedral : 8.506 106.144 2899 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.68 % Allowed : 10.47 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 2516 helix: 1.08 (0.13), residues: 1792 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 314 HIS 0.002 0.000 HIS C 192 PHE 0.011 0.001 PHE D 300 TYR 0.013 0.001 TYR C 36 ARG 0.002 0.000 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 2.426 Fit side-chains REVERT: A 230 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8854 (tt) REVERT: A 409 TRP cc_start: 0.9083 (OUTLIER) cc_final: 0.8278 (m-90) REVERT: A 421 MET cc_start: 0.8073 (tmm) cc_final: 0.7597 (tmm) REVERT: A 441 MET cc_start: 0.8345 (mtm) cc_final: 0.7614 (mtp) REVERT: B 230 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 409 TRP cc_start: 0.9075 (OUTLIER) cc_final: 0.8271 (m-90) REVERT: B 421 MET cc_start: 0.8057 (tmm) cc_final: 0.7598 (tmm) REVERT: B 441 MET cc_start: 0.8351 (mtm) cc_final: 0.7620 (mtp) REVERT: B 753 MET cc_start: 0.7744 (mtp) cc_final: 0.7072 (mmm) REVERT: C 230 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8848 (tt) REVERT: C 409 TRP cc_start: 0.9085 (OUTLIER) cc_final: 0.8278 (m-90) REVERT: C 421 MET cc_start: 0.8074 (tmm) cc_final: 0.7601 (tmm) REVERT: C 441 MET cc_start: 0.8354 (mtm) cc_final: 0.7627 (mtp) REVERT: D 230 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8847 (tt) REVERT: D 409 TRP cc_start: 0.9085 (OUTLIER) cc_final: 0.8276 (m-90) REVERT: D 421 MET cc_start: 0.8071 (tmm) cc_final: 0.7595 (tmm) REVERT: D 441 MET cc_start: 0.8339 (mtm) cc_final: 0.7626 (mtp) outliers start: 38 outliers final: 25 residues processed: 229 average time/residue: 0.2799 time to fit residues: 105.7244 Evaluate side-chains 221 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 420 GLN Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 21576 Z= 0.391 Angle : 0.572 6.281 29235 Z= 0.292 Chirality : 0.040 0.137 3276 Planarity : 0.004 0.047 3619 Dihedral : 8.437 99.528 2899 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.17 % Allowed : 14.23 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2516 helix: 0.90 (0.13), residues: 1812 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 314 HIS 0.003 0.001 HIS B 630 PHE 0.017 0.002 PHE B 300 TYR 0.012 0.002 TYR C 624 ARG 0.004 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 180 time to evaluate : 2.491 Fit side-chains REVERT: A 230 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8885 (tt) REVERT: A 409 TRP cc_start: 0.9184 (OUTLIER) cc_final: 0.8515 (m-90) REVERT: A 421 MET cc_start: 0.8139 (tmm) cc_final: 0.7647 (tmm) REVERT: A 430 ILE cc_start: 0.8800 (mm) cc_final: 0.8575 (mm) REVERT: A 441 MET cc_start: 0.8337 (mtm) cc_final: 0.7651 (mtp) REVERT: B 230 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8881 (tt) REVERT: B 409 TRP cc_start: 0.9180 (OUTLIER) cc_final: 0.8511 (m-90) REVERT: B 421 MET cc_start: 0.8140 (tmm) cc_final: 0.7661 (tmm) REVERT: B 430 ILE cc_start: 0.8803 (mm) cc_final: 0.8580 (mm) REVERT: B 441 MET cc_start: 0.8351 (mtm) cc_final: 0.7657 (mtp) REVERT: C 230 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8882 (tt) REVERT: C 409 TRP cc_start: 0.9186 (OUTLIER) cc_final: 0.8516 (m-90) REVERT: C 421 MET cc_start: 0.8142 (tmm) cc_final: 0.7646 (tmm) REVERT: C 430 ILE cc_start: 0.8800 (mm) cc_final: 0.8572 (mm) REVERT: C 441 MET cc_start: 0.8349 (mtm) cc_final: 0.7658 (mtp) REVERT: D 230 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8880 (tt) REVERT: D 409 TRP cc_start: 0.9189 (OUTLIER) cc_final: 0.8523 (m-90) REVERT: D 421 MET cc_start: 0.8143 (tmm) cc_final: 0.7642 (tmm) REVERT: D 430 ILE cc_start: 0.8795 (mm) cc_final: 0.8567 (mm) REVERT: D 441 MET cc_start: 0.8335 (mtm) cc_final: 0.7663 (mtp) outliers start: 49 outliers final: 24 residues processed: 217 average time/residue: 0.2832 time to fit residues: 100.5191 Evaluate side-chains 217 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 211 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 0.0040 chunk 62 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21576 Z= 0.184 Angle : 0.473 6.271 29235 Z= 0.240 Chirality : 0.036 0.124 3276 Planarity : 0.003 0.048 3619 Dihedral : 7.979 92.709 2896 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.94 % Allowed : 16.08 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 2516 helix: 1.08 (0.13), residues: 1824 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 314 HIS 0.002 0.000 HIS D 192 PHE 0.010 0.001 PHE D 300 TYR 0.011 0.001 TYR A 36 ARG 0.002 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 2.630 Fit side-chains REVERT: A 107 GLU cc_start: 0.7921 (pp20) cc_final: 0.7329 (pp20) REVERT: A 230 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8929 (tt) REVERT: A 409 TRP cc_start: 0.9084 (OUTLIER) cc_final: 0.8480 (m-90) REVERT: A 421 MET cc_start: 0.8126 (tmm) cc_final: 0.7658 (tmm) REVERT: A 441 MET cc_start: 0.8309 (mtm) cc_final: 0.7499 (mtp) REVERT: A 753 MET cc_start: 0.7873 (ttm) cc_final: 0.7451 (ttm) REVERT: B 107 GLU cc_start: 0.7921 (pp20) cc_final: 0.7336 (pp20) REVERT: B 230 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 409 TRP cc_start: 0.9077 (OUTLIER) cc_final: 0.8382 (m-90) REVERT: B 421 MET cc_start: 0.8126 (tmm) cc_final: 0.7680 (tmm) REVERT: B 441 MET cc_start: 0.8318 (mtm) cc_final: 0.7506 (mtp) REVERT: C 107 GLU cc_start: 0.7930 (pp20) cc_final: 0.7348 (pp20) REVERT: C 230 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8931 (tt) REVERT: C 409 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8483 (m-90) REVERT: C 421 MET cc_start: 0.8110 (tmm) cc_final: 0.7648 (tmm) REVERT: C 441 MET cc_start: 0.8320 (mtm) cc_final: 0.7507 (mtp) REVERT: D 107 GLU cc_start: 0.7929 (pp20) cc_final: 0.7348 (pp20) REVERT: D 230 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8928 (tt) REVERT: D 409 TRP cc_start: 0.9088 (OUTLIER) cc_final: 0.8483 (m-90) REVERT: D 421 MET cc_start: 0.8125 (tmm) cc_final: 0.7652 (tmm) REVERT: D 441 MET cc_start: 0.8307 (mtm) cc_final: 0.7511 (mtp) REVERT: D 753 MET cc_start: 0.7775 (mtp) cc_final: 0.7440 (mmm) outliers start: 44 outliers final: 24 residues processed: 234 average time/residue: 0.2769 time to fit residues: 106.3159 Evaluate side-chains 225 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 61 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21576 Z= 0.215 Angle : 0.489 8.449 29235 Z= 0.247 Chirality : 0.036 0.119 3276 Planarity : 0.003 0.047 3619 Dihedral : 7.523 85.121 2896 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.83 % Allowed : 16.97 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2516 helix: 1.08 (0.13), residues: 1828 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 314 HIS 0.002 0.000 HIS A 630 PHE 0.014 0.001 PHE A 335 TYR 0.011 0.001 TYR C 36 ARG 0.002 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 196 time to evaluate : 2.416 Fit side-chains REVERT: A 107 GLU cc_start: 0.7895 (pp20) cc_final: 0.7314 (pp20) REVERT: A 230 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 409 TRP cc_start: 0.9092 (OUTLIER) cc_final: 0.8476 (m-90) REVERT: A 421 MET cc_start: 0.8154 (tmm) cc_final: 0.7703 (tmm) REVERT: A 441 MET cc_start: 0.8254 (mtm) cc_final: 0.7576 (mtp) REVERT: A 753 MET cc_start: 0.7834 (ttm) cc_final: 0.7402 (ttm) REVERT: B 107 GLU cc_start: 0.7898 (pp20) cc_final: 0.7318 (pp20) REVERT: B 230 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8918 (tt) REVERT: B 409 TRP cc_start: 0.9086 (OUTLIER) cc_final: 0.8472 (m-90) REVERT: B 421 MET cc_start: 0.8160 (tmm) cc_final: 0.7696 (tmm) REVERT: B 441 MET cc_start: 0.8260 (mtm) cc_final: 0.7581 (mtp) REVERT: C 107 GLU cc_start: 0.7905 (pp20) cc_final: 0.7335 (pp20) REVERT: C 230 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 409 TRP cc_start: 0.9095 (OUTLIER) cc_final: 0.8478 (m-90) REVERT: C 421 MET cc_start: 0.8160 (tmm) cc_final: 0.7703 (tmm) REVERT: C 441 MET cc_start: 0.8264 (mtm) cc_final: 0.7586 (mtp) REVERT: D 107 GLU cc_start: 0.7905 (pp20) cc_final: 0.7334 (pp20) REVERT: D 230 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8918 (tt) REVERT: D 409 TRP cc_start: 0.9093 (OUTLIER) cc_final: 0.8476 (m-90) REVERT: D 421 MET cc_start: 0.8154 (tmm) cc_final: 0.7701 (tmm) REVERT: D 441 MET cc_start: 0.8249 (mtm) cc_final: 0.7587 (mtp) REVERT: D 753 MET cc_start: 0.7658 (mtp) cc_final: 0.7325 (mmm) outliers start: 64 outliers final: 31 residues processed: 246 average time/residue: 0.2743 time to fit residues: 111.1203 Evaluate side-chains 225 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 186 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 448 THR Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 0.0970 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21576 Z= 0.149 Angle : 0.475 7.488 29235 Z= 0.237 Chirality : 0.035 0.114 3276 Planarity : 0.003 0.046 3619 Dihedral : 7.035 80.346 2896 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.30 % Allowed : 17.63 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2516 helix: 1.29 (0.13), residues: 1804 sheet: None (None), residues: 0 loop : -1.15 (0.26), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 314 HIS 0.002 0.000 HIS D 192 PHE 0.009 0.001 PHE B 300 TYR 0.015 0.001 TYR B 36 ARG 0.002 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 220 time to evaluate : 2.452 Fit side-chains REVERT: A 107 GLU cc_start: 0.7896 (pp20) cc_final: 0.7317 (pp20) REVERT: A 230 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.9007 (tt) REVERT: A 409 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.8484 (m-90) REVERT: A 421 MET cc_start: 0.8116 (tmm) cc_final: 0.7694 (tmm) REVERT: A 441 MET cc_start: 0.8240 (mtm) cc_final: 0.7509 (mtp) REVERT: B 107 GLU cc_start: 0.7903 (pp20) cc_final: 0.7326 (pp20) REVERT: B 230 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 409 TRP cc_start: 0.9026 (OUTLIER) cc_final: 0.8483 (m-90) REVERT: B 421 MET cc_start: 0.8133 (tmm) cc_final: 0.7721 (tmm) REVERT: B 441 MET cc_start: 0.8244 (mtm) cc_final: 0.7513 (mtp) REVERT: C 107 GLU cc_start: 0.7909 (pp20) cc_final: 0.7338 (pp20) REVERT: C 409 TRP cc_start: 0.9032 (OUTLIER) cc_final: 0.8485 (m-90) REVERT: C 421 MET cc_start: 0.8168 (tmm) cc_final: 0.7734 (tmm) REVERT: C 441 MET cc_start: 0.8249 (mtm) cc_final: 0.7516 (mtp) REVERT: D 107 GLU cc_start: 0.7906 (pp20) cc_final: 0.7335 (pp20) REVERT: D 230 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8927 (tt) REVERT: D 409 TRP cc_start: 0.9033 (OUTLIER) cc_final: 0.8490 (m-90) REVERT: D 421 MET cc_start: 0.8164 (tmm) cc_final: 0.7731 (tmm) REVERT: D 441 MET cc_start: 0.8239 (mtm) cc_final: 0.7516 (mtp) REVERT: D 753 MET cc_start: 0.7608 (mtp) cc_final: 0.7288 (mmm) outliers start: 52 outliers final: 26 residues processed: 264 average time/residue: 0.2749 time to fit residues: 119.9963 Evaluate side-chains 229 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 196 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 121 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN B 153 ASN ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN C 153 ASN ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21576 Z= 0.123 Angle : 0.475 7.646 29235 Z= 0.232 Chirality : 0.035 0.115 3276 Planarity : 0.003 0.047 3619 Dihedral : 6.474 74.558 2896 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.59 % Allowed : 18.16 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2516 helix: 1.49 (0.13), residues: 1784 sheet: None (None), residues: 0 loop : -1.33 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.002 0.000 HIS D 192 PHE 0.018 0.001 PHE A 335 TYR 0.012 0.001 TYR C 36 ARG 0.002 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 211 time to evaluate : 2.622 Fit side-chains REVERT: A 107 GLU cc_start: 0.7869 (pp20) cc_final: 0.7292 (pp20) REVERT: A 409 TRP cc_start: 0.8954 (OUTLIER) cc_final: 0.8469 (m-90) REVERT: A 421 MET cc_start: 0.8105 (tmm) cc_final: 0.7714 (tmm) REVERT: A 441 MET cc_start: 0.8157 (mtm) cc_final: 0.7600 (mtp) REVERT: B 107 GLU cc_start: 0.7872 (pp20) cc_final: 0.7297 (pp20) REVERT: B 409 TRP cc_start: 0.8982 (OUTLIER) cc_final: 0.8500 (m-90) REVERT: B 421 MET cc_start: 0.8101 (tmm) cc_final: 0.7702 (tmm) REVERT: B 441 MET cc_start: 0.8171 (mtm) cc_final: 0.7608 (mtp) REVERT: C 107 GLU cc_start: 0.7878 (pp20) cc_final: 0.7315 (pp20) REVERT: C 409 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.8471 (m-90) REVERT: C 421 MET cc_start: 0.8116 (tmm) cc_final: 0.7721 (tmm) REVERT: C 441 MET cc_start: 0.8169 (mtm) cc_final: 0.7608 (mtp) REVERT: D 107 GLU cc_start: 0.7875 (pp20) cc_final: 0.7307 (pp20) REVERT: D 409 TRP cc_start: 0.8958 (OUTLIER) cc_final: 0.8472 (m-90) REVERT: D 421 MET cc_start: 0.8107 (tmm) cc_final: 0.7708 (tmm) REVERT: D 441 MET cc_start: 0.8158 (mtm) cc_final: 0.7605 (mtp) REVERT: D 753 MET cc_start: 0.7538 (mtp) cc_final: 0.7296 (mmm) outliers start: 36 outliers final: 24 residues processed: 242 average time/residue: 0.2962 time to fit residues: 114.8995 Evaluate side-chains 236 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 0.0470 chunk 215 optimal weight: 0.2980 chunk 229 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21576 Z= 0.159 Angle : 0.485 9.833 29235 Z= 0.238 Chirality : 0.035 0.123 3276 Planarity : 0.003 0.048 3619 Dihedral : 6.224 71.305 2896 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.46 % Allowed : 18.47 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 2516 helix: 1.52 (0.13), residues: 1792 sheet: None (None), residues: 0 loop : -1.31 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.004 0.000 HIS B 703 PHE 0.013 0.001 PHE B 521 TYR 0.011 0.001 TYR D 36 ARG 0.002 0.000 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 205 time to evaluate : 2.524 Fit side-chains REVERT: A 107 GLU cc_start: 0.7825 (pp20) cc_final: 0.7297 (pp20) REVERT: A 409 TRP cc_start: 0.8995 (OUTLIER) cc_final: 0.8500 (m-90) REVERT: A 421 MET cc_start: 0.8118 (tmm) cc_final: 0.7715 (tmm) REVERT: A 441 MET cc_start: 0.8121 (mtm) cc_final: 0.7584 (mtp) REVERT: B 107 GLU cc_start: 0.7831 (pp20) cc_final: 0.7307 (pp20) REVERT: B 409 TRP cc_start: 0.9006 (OUTLIER) cc_final: 0.8514 (m-90) REVERT: B 421 MET cc_start: 0.8153 (tmm) cc_final: 0.7752 (tmm) REVERT: B 441 MET cc_start: 0.8125 (mtm) cc_final: 0.7592 (mtp) REVERT: C 107 GLU cc_start: 0.7838 (pp20) cc_final: 0.7316 (pp20) REVERT: C 409 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.8502 (m-90) REVERT: C 421 MET cc_start: 0.8123 (tmm) cc_final: 0.7722 (tmm) REVERT: C 441 MET cc_start: 0.8129 (mtm) cc_final: 0.7591 (mtp) REVERT: D 107 GLU cc_start: 0.7833 (pp20) cc_final: 0.7313 (pp20) REVERT: D 409 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8514 (m-90) REVERT: D 421 MET cc_start: 0.8127 (tmm) cc_final: 0.7719 (tmm) REVERT: D 441 MET cc_start: 0.8149 (mtm) cc_final: 0.7626 (mtp) outliers start: 33 outliers final: 26 residues processed: 231 average time/residue: 0.2952 time to fit residues: 111.8157 Evaluate side-chains 229 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 4.9990 chunk 148 optimal weight: 0.2980 chunk 115 optimal weight: 8.9990 chunk 169 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 234 optimal weight: 0.0770 chunk 203 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21576 Z= 0.135 Angle : 0.480 10.617 29235 Z= 0.234 Chirality : 0.035 0.116 3276 Planarity : 0.003 0.048 3619 Dihedral : 6.033 69.274 2896 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.33 % Allowed : 18.78 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.18), residues: 2516 helix: 1.57 (0.13), residues: 1792 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 314 HIS 0.004 0.000 HIS D 703 PHE 0.018 0.001 PHE C 335 TYR 0.011 0.001 TYR B 36 ARG 0.002 0.000 ARG C 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5032 Ramachandran restraints generated. 2516 Oldfield, 0 Emsley, 2516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 2.594 Fit side-chains REVERT: A 107 GLU cc_start: 0.7819 (pp20) cc_final: 0.7296 (pp20) REVERT: A 409 TRP cc_start: 0.8956 (OUTLIER) cc_final: 0.8542 (m-90) REVERT: A 421 MET cc_start: 0.8109 (tmm) cc_final: 0.7712 (tmm) REVERT: A 441 MET cc_start: 0.8105 (mtm) cc_final: 0.7581 (mtp) REVERT: B 107 GLU cc_start: 0.7826 (pp20) cc_final: 0.7305 (pp20) REVERT: B 409 TRP cc_start: 0.8957 (OUTLIER) cc_final: 0.8546 (m-90) REVERT: B 421 MET cc_start: 0.8076 (tmm) cc_final: 0.7677 (tmm) REVERT: B 441 MET cc_start: 0.8110 (mtm) cc_final: 0.7586 (mtp) REVERT: C 107 GLU cc_start: 0.7835 (pp20) cc_final: 0.7317 (pp20) REVERT: C 409 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.8543 (m-90) REVERT: C 421 MET cc_start: 0.8114 (tmm) cc_final: 0.7715 (tmm) REVERT: C 441 MET cc_start: 0.8111 (mtm) cc_final: 0.7582 (mtp) REVERT: D 107 GLU cc_start: 0.7828 (pp20) cc_final: 0.7310 (pp20) REVERT: D 409 TRP cc_start: 0.8953 (OUTLIER) cc_final: 0.8537 (m-90) REVERT: D 421 MET cc_start: 0.8117 (tmm) cc_final: 0.7716 (tmm) REVERT: D 441 MET cc_start: 0.8101 (mtm) cc_final: 0.7580 (mtp) outliers start: 30 outliers final: 26 residues processed: 236 average time/residue: 0.2962 time to fit residues: 111.5860 Evaluate side-chains 242 residues out of total 2292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 409 TRP Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 368 CYS Chi-restraints excluded: chain C residue 409 TRP Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 734 ASN Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 409 TRP Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 516 ILE Chi-restraints excluded: chain D residue 734 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.103428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080837 restraints weight = 46647.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079916 restraints weight = 27859.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080704 restraints weight = 26390.634| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21576 Z= 0.177 Angle : 0.494 12.158 29235 Z= 0.242 Chirality : 0.036 0.117 3276 Planarity : 0.003 0.048 3619 Dihedral : 5.929 67.278 2896 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.37 % Allowed : 18.96 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2516 helix: 1.57 (0.13), residues: 1804 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.004 0.000 HIS B 703 PHE 0.014 0.001 PHE B 521 TYR 0.011 0.001 TYR C 58 ARG 0.002 0.000 ARG B 715 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.96 seconds wall clock time: 64 minutes 0.19 seconds (3840.19 seconds total)