Starting phenix.real_space_refine on Sun Mar 17 02:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8t_23236/03_2024/7l8t_23236_updated.pdb" } resolution = 3.7 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10171 2.51 5 N 2771 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16337 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3521 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1198 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain: "C" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.96, per 1000 atoms: 0.61 Number of scatterers: 16337 At special positions: 0 Unit cell: (126.69, 135.96, 131.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3290 8.00 N 2771 7.00 C 10171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.05 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.01 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.05 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.10 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 160 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 289 " " NAG A 615 " - " ASN A 137 " " NAG A 616 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 386 " " NAG C 606 " - " ASN C 339 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG C 613 " - " ASN C 355 " " NAG C 614 " - " ASN C 289 " " NAG C 615 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN B 611 " " NAG N 1 " - " ASN C 392 " " NAG O 1 " - " ASN C 332 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 156 " Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 2.5 seconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 33 sheets defined 28.9% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.941A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.356A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 557 removed outlier: 3.831A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 555 " --> pdb=" O GLN B 551 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 557 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 removed outlier: 3.996A pdb=" N LYS B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 634 removed outlier: 4.702A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 662 removed outlier: 5.177A pdb=" N GLN B 640 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 654 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.481A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 352 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.669A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.394A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 532 through 567 removed outlier: 3.761A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 542 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 546 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY D 547 " --> pdb=" O LEU D 544 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 549 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 550 " --> pdb=" O GLY D 547 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 554 " --> pdb=" O GLN D 551 " (cutoff:3.500A) Proline residue: D 559 - end of helix removed outlier: 3.628A pdb=" N GLN D 563 " --> pdb=" O GLU D 560 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 565 " --> pdb=" O GLN D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 621 No H-bonds generated for 'chain 'D' and resid 619 through 621' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 662 removed outlier: 5.015A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 661 " --> pdb=" O GLN D 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 140 through 150 No H-bonds generated for 'chain 'E' and resid 140 through 150' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.520A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'E' and resid 475 through 485 removed outlier: 3.603A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.197A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 530 through 536 removed outlier: 4.660A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 553 removed outlier: 3.751A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 567 removed outlier: 4.211A pdb=" N LYS F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 623 Processing helix chain 'F' and resid 628 through 662 removed outlier: 6.162A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 662 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 93 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.602A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 382 through 385 removed outlier: 4.018A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.873A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.425A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= N, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= P, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.791A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.503A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.860A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.883A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= V, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= X, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= Y, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.383A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 383 through 385 removed outlier: 4.147A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 301 through 303 removed outlier: 4.026A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP E 322 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.559A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 4 through 7 Processing sheet with id= AE, first strand: chain 'H' and resid 112 through 114 removed outlier: 5.806A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 7 through 9 removed outlier: 4.164A pdb=" N UNK L 23 " --> pdb=" O UNK L 9 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.637A pdb=" N UNK L 86 " --> pdb=" O UNK L 39 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N UNK L 36 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N UNK L 38 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N UNK L 47 " --> pdb=" O UNK L 38 " (cutoff:3.500A) 564 hydrogen bonds defined for protein. 1344 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: 5.94 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3135 1.31 - 1.45: 5419 1.45 - 1.60: 7898 1.60 - 1.74: 34 1.74 - 1.88: 129 Bond restraints: 16615 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.422 -0.096 1.10e-02 8.26e+03 7.56e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.93e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.07e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.26e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 16610 not shown) Histogram of bond angle deviations from ideal: 92.27 - 100.81: 15 100.81 - 109.34: 3249 109.34 - 117.87: 10097 117.87 - 126.40: 8964 126.40 - 134.94: 273 Bond angle restraints: 22598 Sorted by residual: angle pdb=" N HIS A 66 " pdb=" CA HIS A 66 " pdb=" C HIS A 66 " ideal model delta sigma weight residual 108.63 92.27 16.36 1.60e+00 3.91e-01 1.05e+02 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 129.13 -9.57 1.02e+00 9.61e-01 8.81e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.97 -9.41 1.02e+00 9.61e-01 8.51e+01 angle pdb=" N GLY A 458 " pdb=" CA GLY A 458 " pdb=" C GLY A 458 " ideal model delta sigma weight residual 111.95 103.91 8.04 9.50e-01 1.11e+00 7.16e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.89 -8.33 1.02e+00 9.61e-01 6.68e+01 ... (remaining 22593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10794 21.23 - 42.47: 260 42.47 - 63.70: 78 63.70 - 84.93: 25 84.93 - 106.17: 16 Dihedral angle restraints: 11173 sinusoidal: 5386 harmonic: 5787 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -154.12 68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.76 -63.76 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.66 -62.66 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 11170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1867 0.100 - 0.200: 603 0.200 - 0.300: 229 0.300 - 0.400: 115 0.400 - 0.500: 48 Chirality restraints: 2862 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 ... (remaining 2859 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 603 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG A 603 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 603 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG A 603 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG A 603 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.328 2.00e-02 2.50e+03 2.80e-01 9.80e+02 pdb=" C7 NAG K 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.492 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.294 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" C7 NAG A 601 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.436 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.202 2.00e-02 2.50e+03 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4585 2.83 - 3.35: 14935 3.35 - 3.86: 25885 3.86 - 4.38: 30469 4.38 - 4.90: 49046 Nonbonded interactions: 124920 Sorted by model distance: nonbonded pdb=" O3 NAG A 615 " pdb=" O7 NAG A 615 " model vdw 2.311 2.440 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.316 2.440 nonbonded pdb=" N UNK H 96 " pdb=" O UNK H 96 " model vdw 2.385 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.391 2.496 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.407 2.496 ... (remaining 124915 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 32 through 503 or resid 601 through 615)) selection = chain 'C' selection = (chain 'E' and (resid 32 through 503 or resid 601 through 615)) } ncs_group { reference = (chain 'B' and (resid 521 through 663 or resid 701 through 702)) selection = (chain 'D' and (resid 521 through 663 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 663 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'H' and resid 16 through 117) selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'S' } 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: 3.170 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: 0.000 Extract box with map and model: 11.670 Check model and map are aligned: 0.220 Set scattering table: 0.180 Process input model: 46.730 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.022 0.127 16615 Z= 1.410 Angle : 1.705 16.357 22598 Z= 1.103 Chirality : 0.139 0.500 2862 Planarity : 0.014 0.294 2784 Dihedral : 11.186 106.168 7303 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.11 % 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 (0.19), residues: 1752 helix: 0.04 (0.21), residues: 478 sheet: 0.95 (0.23), residues: 446 loop : 0.98 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.010 TRP F 623 HIS 0.012 0.003 HIS A 374 PHE 0.035 0.006 PHE A 383 TYR 0.043 0.007 TYR C 40 ARG 0.008 0.001 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.9175 (m-80) cc_final: 0.8960 (m-10) REVERT: B 552 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8335 (mm-40) REVERT: B 575 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8388 (mm110) REVERT: B 626 MET cc_start: 0.8932 (mmm) cc_final: 0.8642 (mmm) REVERT: B 638 TYR cc_start: 0.8869 (m-80) cc_final: 0.8390 (m-10) REVERT: C 99 ASN cc_start: 0.8874 (t0) cc_final: 0.8468 (t0) REVERT: C 102 GLU cc_start: 0.8457 (tp30) cc_final: 0.8091 (tp30) REVERT: C 199 SER cc_start: 0.9500 (p) cc_final: 0.9132 (t) REVERT: C 381 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7292 (mt-10) REVERT: D 536 THR cc_start: 0.8824 (p) cc_final: 0.8526 (p) REVERT: E 65 LYS cc_start: 0.8759 (mttt) cc_final: 0.8551 (UNCLASSIFIED) REVERT: E 91 GLU cc_start: 0.6740 (tp30) cc_final: 0.6330 (tp30) REVERT: E 150 MET cc_start: 0.8445 (mtp) cc_final: 0.8022 (mtt) REVERT: F 530 MET cc_start: 0.7984 (mtp) cc_final: 0.7569 (mtp) REVERT: F 542 ARG cc_start: 0.8334 (mtp180) cc_final: 0.7978 (ttp-170) REVERT: F 560 GLU cc_start: 0.8429 (pm20) cc_final: 0.8223 (pm20) REVERT: F 599 SER cc_start: 0.9214 (t) cc_final: 0.9000 (p) REVERT: F 647 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7184 (mt-10) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.2994 time to fit residues: 183.2365 Evaluate side-chains 215 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN C 85 HIS C 188 ASN C 203 GLN C 352 HIS D 543 ASN D 550 GLN D 551 GLN E 195 ASN E 249 HIS E 422 GLN ** E 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16615 Z= 0.234 Angle : 0.711 14.483 22598 Z= 0.366 Chirality : 0.048 0.376 2862 Planarity : 0.005 0.036 2784 Dihedral : 8.439 80.316 3931 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.92 % Allowed : 9.01 % Favored : 88.07 % 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: 1.04 (0.20), residues: 1752 helix: 0.95 (0.24), residues: 449 sheet: 0.93 (0.24), residues: 417 loop : 0.59 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 628 HIS 0.009 0.001 HIS B 564 PHE 0.031 0.002 PHE E 53 TYR 0.029 0.002 TYR E 61 ARG 0.005 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 261 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 552 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8433 (mm-40) REVERT: B 575 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8203 (mm-40) REVERT: B 615 SER cc_start: 0.8757 (t) cc_final: 0.8336 (p) REVERT: C 102 GLU cc_start: 0.8048 (tp30) cc_final: 0.7845 (tp30) REVERT: C 199 SER cc_start: 0.9406 (p) cc_final: 0.9014 (t) REVERT: C 381 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7131 (mt-10) REVERT: E 39 TYR cc_start: 0.8789 (m-80) cc_final: 0.8585 (m-80) REVERT: E 91 GLU cc_start: 0.6853 (tp30) cc_final: 0.6383 (tp30) REVERT: E 150 MET cc_start: 0.8177 (mtp) cc_final: 0.7812 (mtt) REVERT: F 530 MET cc_start: 0.7891 (mtp) cc_final: 0.7526 (mtp) REVERT: F 545 LEU cc_start: 0.8812 (mt) cc_final: 0.8212 (mt) REVERT: F 616 ASN cc_start: 0.7336 (t0) cc_final: 0.7011 (p0) REVERT: F 622 ILE cc_start: 0.8488 (mt) cc_final: 0.8036 (mt) outliers start: 46 outliers final: 35 residues processed: 294 average time/residue: 0.2997 time to fit residues: 128.3004 Evaluate side-chains 240 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 158 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS E 195 ASN F 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 16615 Z= 0.480 Angle : 0.785 9.874 22598 Z= 0.396 Chirality : 0.051 0.311 2862 Planarity : 0.005 0.048 2784 Dihedral : 8.419 73.438 3931 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.31 % Allowed : 11.10 % Favored : 84.58 % 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: 0.34 (0.20), residues: 1752 helix: 0.30 (0.24), residues: 455 sheet: 0.53 (0.23), residues: 447 loop : 0.17 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 35 HIS 0.010 0.003 HIS B 564 PHE 0.024 0.003 PHE E 53 TYR 0.021 0.002 TYR C 484 ARG 0.005 0.001 ARG E 444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7919 (mm-30) REVERT: B 552 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 553 SER cc_start: 0.8852 (m) cc_final: 0.8646 (t) REVERT: B 575 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8483 (mm-40) REVERT: B 586 TYR cc_start: 0.9553 (t80) cc_final: 0.8963 (t80) REVERT: B 638 TYR cc_start: 0.9016 (m-80) cc_final: 0.8785 (m-10) REVERT: C 199 SER cc_start: 0.9461 (p) cc_final: 0.9033 (t) REVERT: D 545 LEU cc_start: 0.8804 (mt) cc_final: 0.8577 (mt) REVERT: E 91 GLU cc_start: 0.7133 (tp30) cc_final: 0.6583 (tp30) REVERT: E 96 TRP cc_start: 0.8737 (m100) cc_final: 0.8348 (m100) REVERT: E 111 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8884 (mp) REVERT: E 150 MET cc_start: 0.8306 (mtp) cc_final: 0.7900 (mtt) REVERT: F 530 MET cc_start: 0.7988 (mtp) cc_final: 0.7765 (mtp) REVERT: F 562 GLN cc_start: 0.7586 (mm-40) cc_final: 0.6766 (mp10) REVERT: F 616 ASN cc_start: 0.7399 (t0) cc_final: 0.6952 (p0) REVERT: F 622 ILE cc_start: 0.8690 (mt) cc_final: 0.8436 (mt) outliers start: 68 outliers final: 53 residues processed: 262 average time/residue: 0.3476 time to fit residues: 135.2169 Evaluate side-chains 240 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 186 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 658 GLN C 478 ASN E 72 HIS E 195 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16615 Z= 0.188 Angle : 0.587 9.739 22598 Z= 0.297 Chirality : 0.045 0.257 2862 Planarity : 0.004 0.037 2784 Dihedral : 7.440 65.011 3931 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.11 % Allowed : 12.37 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.47 (0.20), residues: 1752 helix: 0.58 (0.26), residues: 449 sheet: 0.61 (0.23), residues: 447 loop : 0.14 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 623 HIS 0.007 0.001 HIS B 564 PHE 0.020 0.002 PHE E 53 TYR 0.017 0.001 TYR E 61 ARG 0.005 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 218 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9225 (m100) cc_final: 0.8577 (m100) REVERT: A 59 LYS cc_start: 0.7942 (tppt) cc_final: 0.7615 (tmtt) REVERT: A 268 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7873 (mm-30) REVERT: A 475 MET cc_start: 0.8497 (mmm) cc_final: 0.8275 (mmm) REVERT: B 552 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8191 (mm-40) REVERT: B 575 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8402 (mm-40) REVERT: B 638 TYR cc_start: 0.8842 (m-80) cc_final: 0.8541 (m-80) REVERT: C 111 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8980 (tp) REVERT: C 199 SER cc_start: 0.9384 (p) cc_final: 0.8875 (t) REVERT: E 91 GLU cc_start: 0.7044 (tp30) cc_final: 0.6536 (tp30) REVERT: E 96 TRP cc_start: 0.8629 (m100) cc_final: 0.8257 (m100) REVERT: E 100 MET cc_start: 0.8955 (mtp) cc_final: 0.8638 (mtp) REVERT: E 111 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8954 (mp) REVERT: E 150 MET cc_start: 0.8219 (mtp) cc_final: 0.7882 (mtt) REVERT: F 530 MET cc_start: 0.7928 (mtp) cc_final: 0.7641 (mtp) REVERT: F 545 LEU cc_start: 0.8814 (mt) cc_final: 0.8276 (mt) REVERT: F 551 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7677 (pt0) REVERT: F 616 ASN cc_start: 0.7453 (t0) cc_final: 0.7063 (p0) REVERT: F 622 ILE cc_start: 0.8552 (mt) cc_final: 0.8322 (mt) outliers start: 49 outliers final: 36 residues processed: 254 average time/residue: 0.2860 time to fit residues: 106.7123 Evaluate side-chains 235 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 196 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 246 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 16615 Z= 0.355 Angle : 0.666 9.840 22598 Z= 0.332 Chirality : 0.047 0.270 2862 Planarity : 0.004 0.054 2784 Dihedral : 7.584 60.004 3931 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.57 % Allowed : 12.56 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.20), residues: 1752 helix: 0.40 (0.25), residues: 461 sheet: 0.44 (0.23), residues: 438 loop : -0.18 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 338 HIS 0.007 0.002 HIS B 564 PHE 0.019 0.002 PHE E 53 TYR 0.017 0.002 TYR E 61 ARG 0.007 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 206 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9268 (m100) cc_final: 0.8520 (m100) REVERT: B 552 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8432 (mm110) REVERT: B 553 SER cc_start: 0.8852 (m) cc_final: 0.8589 (t) REVERT: B 575 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8494 (mm-40) REVERT: B 586 TYR cc_start: 0.9510 (t80) cc_final: 0.9143 (t80) REVERT: B 638 TYR cc_start: 0.8869 (m-80) cc_final: 0.8627 (m-80) REVERT: C 103 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8535 (tm-30) REVERT: C 199 SER cc_start: 0.9445 (p) cc_final: 0.8933 (t) REVERT: C 236 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8482 (p) REVERT: E 96 TRP cc_start: 0.8649 (m100) cc_final: 0.8266 (m100) REVERT: E 111 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9028 (mp) REVERT: E 150 MET cc_start: 0.8271 (mtp) cc_final: 0.7934 (mtt) REVERT: E 376 PHE cc_start: 0.8812 (m-80) cc_final: 0.8522 (m-80) REVERT: F 551 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: F 616 ASN cc_start: 0.7404 (t0) cc_final: 0.7002 (p0) outliers start: 72 outliers final: 54 residues processed: 255 average time/residue: 0.2774 time to fit residues: 105.4378 Evaluate side-chains 252 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 195 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 157 optimal weight: 0.0370 chunk 87 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 99 optimal weight: 0.0270 overall best weight: 0.9518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 16615 Z= 0.200 Angle : 0.567 9.712 22598 Z= 0.286 Chirality : 0.044 0.251 2862 Planarity : 0.004 0.039 2784 Dihedral : 7.019 55.339 3931 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 3.49 % Allowed : 13.96 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.20), residues: 1752 helix: 0.60 (0.26), residues: 454 sheet: 0.40 (0.23), residues: 447 loop : -0.12 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 614 HIS 0.008 0.001 HIS B 564 PHE 0.018 0.002 PHE E 53 TYR 0.016 0.001 TYR D 638 ARG 0.005 0.000 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 207 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9223 (m100) cc_final: 0.8587 (m100) REVERT: A 59 LYS cc_start: 0.8121 (tppt) cc_final: 0.7697 (tmtt) REVERT: A 161 MET cc_start: 0.8362 (tpp) cc_final: 0.8077 (tpp) REVERT: A 475 MET cc_start: 0.8690 (mmm) cc_final: 0.8351 (mmm) REVERT: B 552 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8413 (mm110) REVERT: B 575 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8404 (mm-40) REVERT: B 584 GLU cc_start: 0.8759 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 638 TYR cc_start: 0.8824 (m-80) cc_final: 0.8607 (m-80) REVERT: C 103 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8473 (tm-30) REVERT: C 199 SER cc_start: 0.9415 (p) cc_final: 0.8945 (t) REVERT: C 236 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8503 (p) REVERT: E 96 TRP cc_start: 0.8581 (m100) cc_final: 0.8339 (m100) REVERT: E 111 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8997 (mp) REVERT: E 150 MET cc_start: 0.8193 (mtp) cc_final: 0.7906 (mtt) REVERT: E 376 PHE cc_start: 0.8691 (m-80) cc_final: 0.8483 (m-80) REVERT: F 545 LEU cc_start: 0.8814 (mt) cc_final: 0.8315 (mt) REVERT: F 616 ASN cc_start: 0.7403 (t0) cc_final: 0.7131 (p0) REVERT: F 647 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7323 (mt-10) outliers start: 55 outliers final: 43 residues processed: 246 average time/residue: 0.3172 time to fit residues: 115.7832 Evaluate side-chains 239 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 16615 Z= 0.363 Angle : 0.656 9.798 22598 Z= 0.327 Chirality : 0.047 0.264 2862 Planarity : 0.004 0.042 2784 Dihedral : 7.310 54.870 3931 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 3.68 % Allowed : 14.09 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1752 helix: 0.75 (0.26), residues: 437 sheet: 0.24 (0.24), residues: 437 loop : -0.37 (0.22), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 338 HIS 0.007 0.002 HIS E 374 PHE 0.016 0.002 PHE E 53 TYR 0.016 0.002 TYR E 61 ARG 0.005 0.001 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9289 (m100) cc_final: 0.8532 (m100) REVERT: A 59 LYS cc_start: 0.8242 (tppt) cc_final: 0.7764 (tmtt) REVERT: A 161 MET cc_start: 0.8347 (tpp) cc_final: 0.8110 (tpp) REVERT: B 548 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8845 (mt) REVERT: B 575 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8518 (mm-40) REVERT: B 584 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 638 TYR cc_start: 0.8880 (m-80) cc_final: 0.8647 (m-80) REVERT: C 103 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8545 (tm-30) REVERT: C 199 SER cc_start: 0.9452 (p) cc_final: 0.8934 (t) REVERT: C 236 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8519 (p) REVERT: E 96 TRP cc_start: 0.8623 (m100) cc_final: 0.8349 (m100) REVERT: E 111 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9031 (mp) REVERT: E 150 MET cc_start: 0.8258 (mtp) cc_final: 0.7971 (mtt) REVERT: F 545 LEU cc_start: 0.8828 (mt) cc_final: 0.8368 (mt) REVERT: F 616 ASN cc_start: 0.7410 (t0) cc_final: 0.7117 (p0) REVERT: F 629 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8099 (mp) outliers start: 58 outliers final: 47 residues processed: 234 average time/residue: 0.2744 time to fit residues: 96.2639 Evaluate side-chains 239 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 502 LYS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 543 ASN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS E 377 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 16615 Z= 0.164 Angle : 0.551 9.684 22598 Z= 0.278 Chirality : 0.043 0.251 2862 Planarity : 0.004 0.034 2784 Dihedral : 6.639 56.333 3931 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 2.86 % Allowed : 15.61 % Favored : 81.54 % 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: 0.21 (0.20), residues: 1752 helix: 0.92 (0.26), residues: 435 sheet: 0.38 (0.24), residues: 448 loop : -0.31 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 614 HIS 0.008 0.001 HIS D 564 PHE 0.017 0.001 PHE E 53 TYR 0.017 0.001 TYR D 638 ARG 0.006 0.000 ARG D 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9273 (m100) cc_final: 0.8567 (m100) REVERT: A 59 LYS cc_start: 0.8096 (tppt) cc_final: 0.7675 (tmtt) REVERT: A 161 MET cc_start: 0.8346 (tpp) cc_final: 0.8074 (tpp) REVERT: B 548 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 552 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8343 (mm110) REVERT: B 575 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8474 (mm-40) REVERT: B 638 TYR cc_start: 0.8811 (m-80) cc_final: 0.8569 (m-80) REVERT: C 103 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8552 (tm-30) REVERT: C 199 SER cc_start: 0.9410 (p) cc_final: 0.8979 (t) REVERT: E 96 TRP cc_start: 0.8549 (m100) cc_final: 0.8346 (m100) REVERT: E 111 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8966 (mp) REVERT: E 150 MET cc_start: 0.8113 (mtp) cc_final: 0.7904 (mtt) REVERT: F 545 LEU cc_start: 0.8778 (mt) cc_final: 0.8315 (mt) REVERT: F 616 ASN cc_start: 0.7458 (t0) cc_final: 0.7224 (p0) REVERT: F 647 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7295 (mt-10) outliers start: 45 outliers final: 39 residues processed: 242 average time/residue: 0.2812 time to fit residues: 100.2228 Evaluate side-chains 239 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 198 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.4980 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 16615 Z= 0.210 Angle : 0.562 9.728 22598 Z= 0.282 Chirality : 0.044 0.251 2862 Planarity : 0.004 0.035 2784 Dihedral : 6.543 57.551 3931 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 3.05 % Allowed : 15.67 % Favored : 81.28 % 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: 0.20 (0.20), residues: 1752 helix: 0.91 (0.26), residues: 437 sheet: 0.35 (0.24), residues: 448 loop : -0.30 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 614 HIS 0.005 0.001 HIS E 374 PHE 0.015 0.002 PHE E 53 TYR 0.017 0.001 TYR F 638 ARG 0.005 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9266 (m100) cc_final: 0.8622 (m100) REVERT: A 161 MET cc_start: 0.8321 (tpp) cc_final: 0.8043 (tpp) REVERT: B 548 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8687 (mt) REVERT: B 575 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8495 (mm-40) REVERT: B 638 TYR cc_start: 0.8797 (m-80) cc_final: 0.8538 (m-80) REVERT: C 103 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 199 SER cc_start: 0.9442 (p) cc_final: 0.8994 (t) REVERT: C 236 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8526 (p) REVERT: E 111 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8980 (mp) REVERT: E 150 MET cc_start: 0.8164 (mtp) cc_final: 0.7927 (mtt) REVERT: F 545 LEU cc_start: 0.8819 (mt) cc_final: 0.8375 (mt) REVERT: F 616 ASN cc_start: 0.7444 (t0) cc_final: 0.7194 (p0) REVERT: F 629 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8137 (mp) outliers start: 48 outliers final: 41 residues processed: 235 average time/residue: 0.2818 time to fit residues: 97.9213 Evaluate side-chains 240 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 195 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16615 Z= 0.184 Angle : 0.555 9.685 22598 Z= 0.280 Chirality : 0.044 0.250 2862 Planarity : 0.004 0.035 2784 Dihedral : 6.386 58.351 3931 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.09 % Rotamer: Outliers : 2.98 % Allowed : 16.05 % Favored : 80.96 % 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: 0.18 (0.20), residues: 1752 helix: 0.84 (0.26), residues: 443 sheet: 0.34 (0.24), residues: 448 loop : -0.29 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 96 HIS 0.005 0.001 HIS D 564 PHE 0.016 0.001 PHE E 53 TYR 0.023 0.001 TYR F 638 ARG 0.006 0.000 ARG D 557 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9268 (m100) cc_final: 0.8633 (m100) REVERT: A 59 LYS cc_start: 0.8238 (tppt) cc_final: 0.7665 (tmtt) REVERT: A 161 MET cc_start: 0.8320 (tpp) cc_final: 0.8040 (tpp) REVERT: B 548 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8698 (mt) REVERT: B 638 TYR cc_start: 0.8793 (m-80) cc_final: 0.8555 (m-80) REVERT: C 103 GLN cc_start: 0.8911 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 236 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8522 (p) REVERT: E 111 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8965 (mp) REVERT: E 150 MET cc_start: 0.8121 (mtp) cc_final: 0.7902 (mtt) REVERT: F 545 LEU cc_start: 0.8799 (mt) cc_final: 0.8409 (mt) REVERT: F 616 ASN cc_start: 0.7438 (t0) cc_final: 0.7202 (p0) outliers start: 47 outliers final: 39 residues processed: 237 average time/residue: 0.2759 time to fit residues: 97.5560 Evaluate side-chains 238 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 618 ASN Chi-restraints excluded: chain F residue 629 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.097173 restraints weight = 28193.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.099724 restraints weight = 17942.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101452 restraints weight = 13383.338| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 16615 Z= 0.233 Angle : 0.576 9.710 22598 Z= 0.289 Chirality : 0.045 0.286 2862 Planarity : 0.004 0.035 2784 Dihedral : 6.467 57.624 3931 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 2.92 % Allowed : 16.37 % Favored : 80.71 % 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: 0.14 (0.20), residues: 1752 helix: 0.80 (0.26), residues: 445 sheet: 0.32 (0.24), residues: 446 loop : -0.32 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 96 HIS 0.006 0.001 HIS E 374 PHE 0.015 0.002 PHE E 53 TYR 0.017 0.001 TYR F 638 ARG 0.005 0.000 ARG D 557 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3062.40 seconds wall clock time: 56 minutes 24.50 seconds (3384.50 seconds total)