Starting phenix.real_space_refine on Sat Mar 16 19:31:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8u_23237/03_2024/7l8u_23237_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 9639 2.51 5 N 2626 2.21 5 O 3106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 466": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15475 Number of models: 1 Model: "" Number of chains: 25 Chain: "C" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3401 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 4 Chain: "D" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3459 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1006 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3410 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 20, 'TRANS': 410} Chain breaks: 4 Chain: "F" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 565 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'TRANS': 112} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 339 Unresolved non-hydrogen dihedrals: 113 Planarities with less than four sites: {'UNK:plan-1': 113} Unresolved non-hydrogen planarities: 113 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 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: 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: "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: 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "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: "A" 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: "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: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.97, per 1000 atoms: 0.52 Number of scatterers: 15475 At special positions: 0 Unit cell: (128.75, 134.93, 133.9, 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 104 16.00 O 3106 8.00 N 2626 7.00 C 9639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.13 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 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 228 " - pdb=" SG CYS C 239 " distance=2.09 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.18 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.12 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.15 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 7 " " MAN P 4 " - " MAN P 5 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 332 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 301 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 197 " " NAG A 613 " - " ASN A 133 " " NAG A 614 " - " ASN A 355 " " NAG A 615 " - " ASN A 289 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 625 " " 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 392 " " NAG C 606 " - " ASN C 339 " " NAG C 607 " - " ASN C 332 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 241 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 392 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 160 " " NAG E 610 " - " ASN E 197 " " NAG E 611 " - " ASN E 133 " " NAG E 612 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 386 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN C 156 " " NAG K 1 " - " ASN A 386 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN B 618 " " NAG P 1 " - " ASN B 611 " " NAG Q 1 " - " ASN E 88 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 156 " Time building additional restraints: 6.23 Conformation dependent library (CDL) restraints added in 2.4 seconds 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 33 sheets defined 25.1% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'C' and resid 99 through 117 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 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.506A 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 353 removed outlier: 3.864A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) 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 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.592A pdb=" N TRP C 479 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 535 removed outlier: 3.876A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 562 through 565 Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 621 through 624 No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.672A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 662 Processing helix chain 'A' and resid 99 through 117 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 341 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.760A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' 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 482 Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.798A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 No H-bonds generated for 'chain 'B' and resid 538 through 541' Processing helix chain 'B' and resid 564 through 567 Processing helix chain 'B' and resid 571 through 595 Processing helix chain 'B' and resid 619 through 623 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 640 through 657 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 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 351 removed outlier: 4.960A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (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 475 through 483 Processing helix chain 'F' and resid 532 through 535 removed outlier: 4.101A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 537 through 541 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.506A pdb=" N GLN F 577 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 661 removed outlier: 5.128A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN F 652 " --> pdb=" O SER F 649 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS F 655 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN F 658 " --> pdb=" O LYS F 655 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP F 659 " --> pdb=" O ASN F 656 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 660 " --> pdb=" O GLU F 657 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU F 661 " --> pdb=" O GLN F 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.118A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 444 through 449 removed outlier: 4.002A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.082A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.391A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.764A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= N, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= O, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= P, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.914A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.196A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.858A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.172A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= V, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.692A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= Y, first strand: chain 'E' and resid 130 through 133 Processing sheet with id= Z, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= AA, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.501A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.748A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 443 through 449 removed outlier: 3.995A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 358 through 362 Processing sheet with id= AE, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.750A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.537A pdb=" N UNK H 79 " --> pdb=" O UNK H 19 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N UNK H 74 " --> pdb=" O UNK H 70 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 92 through 96 removed outlier: 4.630A pdb=" N UNK H 92 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK H 103 " --> pdb=" O UNK H 96 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1170 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: 5.90 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4538 1.34 - 1.48: 4593 1.48 - 1.63: 6463 1.63 - 1.78: 44 1.78 - 1.93: 99 Bond restraints: 15737 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.99e+01 bond pdb=" NE ARG A 30 " pdb=" CZ ARG A 30 " ideal model delta sigma weight residual 1.326 1.401 -0.075 1.10e-02 8.26e+03 4.63e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.664 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" CB LEU F 544 " pdb=" CG LEU F 544 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.99e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 15732 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.05: 281 105.05 - 112.35: 8083 112.35 - 119.66: 6036 119.66 - 126.96: 6753 126.96 - 134.27: 248 Bond angle restraints: 21401 Sorted by residual: angle pdb=" C ASN A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta sigma weight residual 119.78 127.75 -7.97 1.03e+00 9.43e-01 5.99e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.01e+00 9.80e-01 5.88e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.31 7.16 9.60e-01 1.09e+00 5.57e+01 angle pdb=" N ALA B 525 " pdb=" CA ALA B 525 " pdb=" C ALA B 525 " ideal model delta sigma weight residual 114.39 103.79 10.60 1.45e+00 4.76e-01 5.34e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 126.75 -7.19 1.02e+00 9.61e-01 4.96e+01 ... (remaining 21396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 10168 21.79 - 43.57: 242 43.57 - 65.36: 73 65.36 - 87.14: 40 87.14 - 108.93: 13 Dihedral angle restraints: 10536 sinusoidal: 5049 harmonic: 5487 Sorted by residual: 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 93.00 167.30 -74.30 1 1.00e+01 1.00e-02 7.00e+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 93.00 162.29 -69.29 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.40 -57.40 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1800 0.105 - 0.209: 566 0.209 - 0.314: 207 0.314 - 0.418: 89 0.418 - 0.523: 48 Chirality restraints: 2710 Sorted by residual: chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.82e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.29e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.29e+02 ... (remaining 2707 not shown) Planarity restraints: 2689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 601 " -0.351 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C 601 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 601 " -0.127 2.00e-02 2.50e+03 pdb=" N2 NAG C 601 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C 601 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " -0.340 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A 601 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " 0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " -0.315 2.00e-02 2.50e+03 2.68e-01 8.95e+02 pdb=" C7 NAG C 602 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " 0.466 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " -0.052 2.00e-02 2.50e+03 ... (remaining 2686 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2028 2.74 - 3.28: 15017 3.28 - 3.82: 24487 3.82 - 4.36: 31115 4.36 - 4.90: 48111 Nonbonded interactions: 120758 Sorted by model distance: nonbonded pdb=" O3 NAG B 702 " pdb=" O7 NAG B 702 " model vdw 2.199 2.440 nonbonded pdb=" O ASN B 616 " pdb=" OD1 ASN B 616 " model vdw 2.325 3.040 nonbonded pdb=" CB TRP D 623 " pdb=" N ASP D 624 " model vdw 2.336 2.816 nonbonded pdb=" N ALA B 525 " pdb=" N ALA B 526 " model vdw 2.401 2.560 nonbonded pdb=" N ASP D 664 " pdb=" OD1 ASP D 664 " model vdw 2.407 2.520 ... (remaining 120753 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 34 through 185 or resid 189 through 396 or resid 414 throu \ gh 456 or resid 462 through 502 or resid 601 through 612)) selection = (chain 'C' and (resid 34 through 56 or resid 66 through 185 or resid 189 through \ 456 or resid 462 through 502 or resid 601 through 612)) selection = (chain 'E' and (resid 34 through 56 or resid 66 through 396 or resid 414 through \ 502 or resid 601 through 612)) } ncs_group { reference = (chain 'B' and (resid 521 through 544 or resid 569 through 658)) selection = (chain 'D' and (resid 521 through 544 or resid 569 through 658)) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'H' and resid 10 through 114) selection = chain 'L' } ncs_group { reference = chain 'M' 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: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.630 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 42.160 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.134 15737 Z= 1.334 Angle : 1.769 11.043 21401 Z= 1.131 Chirality : 0.141 0.523 2710 Planarity : 0.015 0.302 2630 Dihedral : 12.079 108.930 6863 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 0.24 (0.20), residues: 1635 helix: -0.27 (0.25), residues: 388 sheet: 0.58 (0.24), residues: 407 loop : 0.32 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.009 TRP A 479 HIS 0.014 0.003 HIS B 564 PHE 0.033 0.006 PHE E 93 TYR 0.079 0.009 TYR A 39 ARG 0.010 0.001 ARG E 308 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8798 (m-80) cc_final: 0.8498 (m-10) REVERT: C 69 TRP cc_start: 0.8966 (m-90) cc_final: 0.8478 (m-90) REVERT: C 91 GLU cc_start: 0.8312 (tp30) cc_final: 0.7799 (tp30) REVERT: C 116 LEU cc_start: 0.9610 (mt) cc_final: 0.9357 (pp) REVERT: D 569 THR cc_start: 0.8825 (p) cc_final: 0.8419 (p) REVERT: D 584 GLU cc_start: 0.9555 (mt-10) cc_final: 0.9289 (mt-10) REVERT: D 585 ARG cc_start: 0.9285 (mtp180) cc_final: 0.9070 (ttm-80) REVERT: D 590 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8917 (mm110) REVERT: D 598 CYS cc_start: 0.8568 (m) cc_final: 0.7918 (m) REVERT: A 95 MET cc_start: 0.9251 (ptm) cc_final: 0.9028 (ptm) REVERT: A 155 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8944 (mtpt) REVERT: A 284 ILE cc_start: 0.9568 (mt) cc_final: 0.9329 (mp) REVERT: A 381 GLU cc_start: 0.9148 (tp30) cc_final: 0.8769 (tp30) REVERT: B 530 MET cc_start: 0.8897 (mtm) cc_final: 0.8343 (mtm) REVERT: B 599 SER cc_start: 0.8506 (p) cc_final: 0.8219 (t) REVERT: E 80 ASN cc_start: 0.8408 (t0) cc_final: 0.8040 (p0) REVERT: E 212 PRO cc_start: 0.9079 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: E 490 LYS cc_start: 0.9427 (pttt) cc_final: 0.9117 (ptmt) REVERT: E 491 ILE cc_start: 0.9793 (mm) cc_final: 0.9410 (mm) REVERT: F 629 LEU cc_start: 0.9275 (mt) cc_final: 0.9075 (tp) REVERT: F 630 GLN cc_start: 0.9239 (mt0) cc_final: 0.9027 (mt0) REVERT: F 631 TRP cc_start: 0.9063 (t60) cc_final: 0.8857 (t60) REVERT: F 651 ASN cc_start: 0.8480 (m-40) cc_final: 0.7250 (m110) REVERT: F 654 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8342 (mt-10) outliers start: 0 outliers final: 0 residues processed: 493 average time/residue: 0.3228 time to fit residues: 222.1400 Evaluate side-chains 250 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 130 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS E 82 GLN ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 658 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15737 Z= 0.245 Angle : 0.771 13.687 21401 Z= 0.398 Chirality : 0.049 0.336 2710 Planarity : 0.004 0.042 2630 Dihedral : 8.946 84.509 3688 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 0.07 % Allowed : 3.22 % Favored : 96.72 % 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: 0.26 (0.20), residues: 1635 helix: 0.54 (0.27), residues: 369 sheet: 0.55 (0.23), residues: 462 loop : -0.12 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 610 HIS 0.007 0.001 HIS A 249 PHE 0.029 0.002 PHE E 376 TYR 0.037 0.003 TYR A 39 ARG 0.009 0.001 ARG E 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.8777 (m-90) cc_final: 0.8288 (m-90) REVERT: C 107 ASP cc_start: 0.9481 (m-30) cc_final: 0.9210 (m-30) REVERT: C 435 TYR cc_start: 0.8730 (t80) cc_final: 0.8506 (t80) REVERT: D 530 MET cc_start: 0.7823 (mtt) cc_final: 0.7398 (ppp) REVERT: D 584 GLU cc_start: 0.9423 (mt-10) cc_final: 0.8927 (tm-30) REVERT: D 593 LEU cc_start: 0.9617 (mt) cc_final: 0.9352 (tp) REVERT: D 596 TRP cc_start: 0.9059 (m-10) cc_final: 0.8670 (m-10) REVERT: D 628 TRP cc_start: 0.6831 (m100) cc_final: 0.6088 (m100) REVERT: D 647 GLU cc_start: 0.8956 (pp20) cc_final: 0.8740 (pp20) REVERT: D 655 LYS cc_start: 0.9183 (ptpt) cc_final: 0.8935 (pttt) REVERT: D 659 ASP cc_start: 0.8271 (m-30) cc_final: 0.8029 (m-30) REVERT: A 155 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9018 (mmtm) REVERT: A 381 GLU cc_start: 0.9219 (tp30) cc_final: 0.9008 (tp30) REVERT: A 426 MET cc_start: 0.8766 (tpt) cc_final: 0.8495 (mmm) REVERT: A 487 LYS cc_start: 0.9237 (ttmm) cc_final: 0.9001 (ttmm) REVERT: B 530 MET cc_start: 0.8458 (mtm) cc_final: 0.8199 (mtm) REVERT: B 629 LEU cc_start: 0.9346 (mp) cc_final: 0.9051 (mm) REVERT: E 37 THR cc_start: 0.8963 (m) cc_final: 0.8540 (p) REVERT: E 80 ASN cc_start: 0.8421 (t0) cc_final: 0.8050 (p0) REVERT: E 91 GLU cc_start: 0.7608 (tp30) cc_final: 0.6400 (tp30) REVERT: E 150 MET cc_start: 0.8942 (mmp) cc_final: 0.8680 (mmm) REVERT: E 227 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8762 (tmtt) REVERT: E 249 HIS cc_start: 0.8741 (p90) cc_final: 0.8425 (p90) REVERT: F 586 TYR cc_start: 0.9226 (t80) cc_final: 0.8946 (t80) REVERT: F 638 TYR cc_start: 0.8888 (m-80) cc_final: 0.8184 (m-80) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.2786 time to fit residues: 138.4401 Evaluate side-chains 219 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS C 203 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS E 352 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 15737 Z= 0.505 Angle : 0.940 9.847 21401 Z= 0.468 Chirality : 0.051 0.295 2710 Planarity : 0.006 0.068 2630 Dihedral : 9.183 82.329 3688 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1635 helix: -0.15 (0.26), residues: 368 sheet: 0.14 (0.25), residues: 427 loop : -0.83 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 610 HIS 0.009 0.002 HIS C 72 PHE 0.055 0.003 PHE A 361 TYR 0.029 0.003 TYR E 39 ARG 0.011 0.001 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.9047 (m-90) cc_final: 0.8799 (m-90) REVERT: C 95 MET cc_start: 0.9373 (ptm) cc_final: 0.7873 (ppp) REVERT: C 217 TYR cc_start: 0.9076 (m-80) cc_final: 0.8863 (m-80) REVERT: C 479 TRP cc_start: 0.8910 (m-10) cc_final: 0.8595 (m-10) REVERT: D 530 MET cc_start: 0.7871 (mtt) cc_final: 0.7512 (ppp) REVERT: D 584 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9033 (tm-30) REVERT: D 585 ARG cc_start: 0.9406 (tpp80) cc_final: 0.9106 (tpp80) REVERT: D 593 LEU cc_start: 0.9728 (mt) cc_final: 0.9428 (tp) REVERT: D 596 TRP cc_start: 0.9308 (m-10) cc_final: 0.8378 (m-10) REVERT: D 628 TRP cc_start: 0.6415 (m100) cc_final: 0.5393 (m100) REVERT: D 654 GLU cc_start: 0.8966 (tt0) cc_final: 0.8687 (tt0) REVERT: A 116 LEU cc_start: 0.9592 (mt) cc_final: 0.9359 (tt) REVERT: A 161 MET cc_start: 0.9303 (tpp) cc_final: 0.8485 (tmm) REVERT: A 177 TYR cc_start: 0.8998 (m-80) cc_final: 0.8720 (m-80) REVERT: A 290 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8509 (mp0) REVERT: A 294 ILE cc_start: 0.8903 (tt) cc_final: 0.8480 (tt) REVERT: B 530 MET cc_start: 0.8269 (mtm) cc_final: 0.8020 (mtt) REVERT: B 573 ILE cc_start: 0.9651 (mt) cc_final: 0.9424 (tt) REVERT: B 626 MET cc_start: 0.8836 (tpt) cc_final: 0.8545 (tpp) REVERT: B 629 LEU cc_start: 0.9365 (mp) cc_final: 0.9066 (mm) REVERT: B 647 GLU cc_start: 0.9019 (pp20) cc_final: 0.8665 (pp20) REVERT: B 654 GLU cc_start: 0.9136 (tp30) cc_final: 0.8911 (tp30) REVERT: B 655 LYS cc_start: 0.9037 (mttt) cc_final: 0.8794 (tptp) REVERT: E 80 ASN cc_start: 0.8722 (t0) cc_final: 0.8233 (p0) REVERT: E 91 GLU cc_start: 0.8188 (tp30) cc_final: 0.6921 (tp30) REVERT: E 104 MET cc_start: 0.9081 (tpp) cc_final: 0.8633 (tpp) REVERT: E 150 MET cc_start: 0.9091 (mmp) cc_final: 0.8859 (mmm) REVERT: E 155 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8521 (tptt) REVERT: E 161 MET cc_start: 0.8586 (tmm) cc_final: 0.7876 (tmm) REVERT: E 211 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8071 (tm-30) REVERT: E 217 TYR cc_start: 0.8685 (m-80) cc_final: 0.7705 (m-80) REVERT: E 286 VAL cc_start: 0.9510 (t) cc_final: 0.9165 (p) REVERT: F 603 ILE cc_start: 0.8769 (mp) cc_final: 0.8447 (mp) REVERT: F 621 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8162 (mt-10) REVERT: F 622 ILE cc_start: 0.8638 (mm) cc_final: 0.8336 (mm) outliers start: 2 outliers final: 0 residues processed: 250 average time/residue: 0.2776 time to fit residues: 101.0225 Evaluate side-chains 187 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 15737 Z= 0.284 Angle : 0.701 8.869 21401 Z= 0.354 Chirality : 0.048 0.518 2710 Planarity : 0.004 0.041 2630 Dihedral : 8.430 79.413 3688 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % 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: -0.59 (0.20), residues: 1635 helix: 0.05 (0.26), residues: 371 sheet: 0.11 (0.25), residues: 434 loop : -0.81 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP F 610 HIS 0.004 0.001 HIS E 105 PHE 0.015 0.002 PHE A 361 TYR 0.027 0.002 TYR A 39 ARG 0.005 0.001 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 251 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.9040 (m-90) cc_final: 0.8814 (m-90) REVERT: D 530 MET cc_start: 0.7861 (mtt) cc_final: 0.7620 (ppp) REVERT: D 577 GLN cc_start: 0.9098 (pp30) cc_final: 0.8856 (pp30) REVERT: D 584 GLU cc_start: 0.9435 (mt-10) cc_final: 0.8931 (tm-30) REVERT: D 585 ARG cc_start: 0.9402 (tpp80) cc_final: 0.9084 (tpp80) REVERT: D 593 LEU cc_start: 0.9683 (mt) cc_final: 0.9411 (tp) REVERT: D 596 TRP cc_start: 0.9231 (m-10) cc_final: 0.8333 (m-10) REVERT: D 628 TRP cc_start: 0.6248 (m100) cc_final: 0.5294 (m100) REVERT: D 652 GLN cc_start: 0.9093 (mm-40) cc_final: 0.8847 (mm-40) REVERT: D 655 LYS cc_start: 0.9361 (pttt) cc_final: 0.9119 (pttp) REVERT: A 95 MET cc_start: 0.9550 (ptm) cc_final: 0.8018 (ppp) REVERT: A 377 ASN cc_start: 0.9014 (t0) cc_final: 0.8811 (t0) REVERT: A 381 GLU cc_start: 0.9170 (tp30) cc_final: 0.8413 (tp30) REVERT: A 426 MET cc_start: 0.8851 (tpt) cc_final: 0.8169 (tmm) REVERT: B 530 MET cc_start: 0.8290 (mtm) cc_final: 0.7887 (mtm) REVERT: B 573 ILE cc_start: 0.9656 (mt) cc_final: 0.9442 (tt) REVERT: B 647 GLU cc_start: 0.8958 (pp20) cc_final: 0.8555 (pp20) REVERT: B 654 GLU cc_start: 0.9087 (tp30) cc_final: 0.8857 (tp30) REVERT: E 80 ASN cc_start: 0.8768 (t0) cc_final: 0.8279 (p0) REVERT: E 91 GLU cc_start: 0.8024 (tp30) cc_final: 0.6783 (tp30) REVERT: E 104 MET cc_start: 0.9201 (tpp) cc_final: 0.8501 (tpp) REVERT: E 150 MET cc_start: 0.9074 (mmp) cc_final: 0.8851 (mmm) REVERT: E 155 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8153 (mmmt) REVERT: E 211 GLU cc_start: 0.8394 (tm-30) cc_final: 0.8045 (tm-30) REVERT: E 217 TYR cc_start: 0.8668 (m-80) cc_final: 0.7647 (m-80) REVERT: E 286 VAL cc_start: 0.9487 (t) cc_final: 0.9196 (p) REVERT: E 474 ASP cc_start: 0.8497 (t0) cc_final: 0.8166 (t0) outliers start: 2 outliers final: 2 residues processed: 253 average time/residue: 0.2818 time to fit residues: 103.5039 Evaluate side-chains 198 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15737 Z= 0.283 Angle : 0.683 9.166 21401 Z= 0.344 Chirality : 0.047 0.499 2710 Planarity : 0.004 0.043 2630 Dihedral : 7.992 77.578 3688 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.07 % Allowed : 3.02 % Favored : 96.92 % 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: -0.65 (0.20), residues: 1635 helix: 0.22 (0.27), residues: 365 sheet: 0.04 (0.24), residues: 452 loop : -0.96 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 610 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.002 PHE A 361 TYR 0.036 0.002 TYR A 39 ARG 0.006 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TRP cc_start: 0.9082 (m-90) cc_final: 0.8833 (m-90) REVERT: C 446 VAL cc_start: 0.8837 (t) cc_final: 0.8621 (t) REVERT: D 522 PHE cc_start: 0.8807 (t80) cc_final: 0.8473 (t80) REVERT: D 584 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8917 (tm-30) REVERT: D 585 ARG cc_start: 0.9421 (tpp80) cc_final: 0.9133 (tpp80) REVERT: D 593 LEU cc_start: 0.9682 (mt) cc_final: 0.9431 (tp) REVERT: D 596 TRP cc_start: 0.9197 (m-10) cc_final: 0.8329 (m-10) REVERT: D 652 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8884 (mm-40) REVERT: A 95 MET cc_start: 0.9527 (ptm) cc_final: 0.7845 (ppp) REVERT: A 177 TYR cc_start: 0.8995 (m-80) cc_final: 0.8637 (m-80) REVERT: A 377 ASN cc_start: 0.9124 (t0) cc_final: 0.8843 (t0) REVERT: A 381 GLU cc_start: 0.9158 (tp30) cc_final: 0.8432 (tp30) REVERT: B 530 MET cc_start: 0.8266 (mtm) cc_final: 0.7603 (mtt) REVERT: B 538 THR cc_start: 0.9440 (p) cc_final: 0.9198 (p) REVERT: B 577 GLN cc_start: 0.8952 (tm130) cc_final: 0.8737 (tm-30) REVERT: B 628 TRP cc_start: 0.8369 (m100) cc_final: 0.7217 (m100) REVERT: B 647 GLU cc_start: 0.8981 (pp20) cc_final: 0.8529 (pp20) REVERT: B 654 GLU cc_start: 0.9063 (tp30) cc_final: 0.8808 (tp30) REVERT: B 655 LYS cc_start: 0.9059 (mttt) cc_final: 0.8823 (tptp) REVERT: E 80 ASN cc_start: 0.8851 (t0) cc_final: 0.8342 (p0) REVERT: E 217 TYR cc_start: 0.8668 (m-80) cc_final: 0.8268 (m-10) REVERT: E 474 ASP cc_start: 0.8662 (t0) cc_final: 0.8403 (t0) REVERT: F 536 THR cc_start: 0.9098 (p) cc_final: 0.8832 (t) REVERT: F 621 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7842 (mt-10) outliers start: 1 outliers final: 1 residues processed: 245 average time/residue: 0.2676 time to fit residues: 96.6175 Evaluate side-chains 194 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN C 188 ASN D 543 ASN A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 HIS B 577 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15737 Z= 0.229 Angle : 0.632 9.237 21401 Z= 0.320 Chirality : 0.045 0.498 2710 Planarity : 0.004 0.041 2630 Dihedral : 7.496 74.800 3688 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1635 helix: 0.29 (0.27), residues: 369 sheet: 0.10 (0.24), residues: 463 loop : -0.87 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 479 HIS 0.005 0.001 HIS A 105 PHE 0.027 0.002 PHE E 376 TYR 0.024 0.002 TYR A 39 ARG 0.009 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 50 THR cc_start: 0.8911 (m) cc_final: 0.8646 (m) REVERT: C 69 TRP cc_start: 0.9009 (m-90) cc_final: 0.8637 (m-90) REVERT: C 107 ASP cc_start: 0.9389 (m-30) cc_final: 0.9023 (m-30) REVERT: C 217 TYR cc_start: 0.9166 (m-80) cc_final: 0.8792 (m-80) REVERT: C 446 VAL cc_start: 0.8899 (t) cc_final: 0.8683 (t) REVERT: D 522 PHE cc_start: 0.8798 (t80) cc_final: 0.8220 (t80) REVERT: D 577 GLN cc_start: 0.9049 (pp30) cc_final: 0.8751 (pp30) REVERT: D 584 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8902 (tm-30) REVERT: D 585 ARG cc_start: 0.9400 (tpp80) cc_final: 0.9131 (tpp80) REVERT: D 593 LEU cc_start: 0.9660 (mt) cc_final: 0.9433 (tp) REVERT: D 596 TRP cc_start: 0.9234 (m-10) cc_final: 0.8331 (m-10) REVERT: A 42 VAL cc_start: 0.9534 (t) cc_final: 0.9250 (p) REVERT: A 95 MET cc_start: 0.9336 (ptm) cc_final: 0.8249 (ppp) REVERT: A 177 TYR cc_start: 0.9011 (m-80) cc_final: 0.8645 (m-80) REVERT: A 377 ASN cc_start: 0.9092 (t0) cc_final: 0.8837 (t0) REVERT: A 381 GLU cc_start: 0.9118 (tp30) cc_final: 0.8333 (tp30) REVERT: B 530 MET cc_start: 0.8246 (mtm) cc_final: 0.6988 (mtt) REVERT: B 538 THR cc_start: 0.9426 (p) cc_final: 0.9160 (p) REVERT: B 577 GLN cc_start: 0.8928 (tm130) cc_final: 0.8714 (tm-30) REVERT: B 626 MET cc_start: 0.8667 (tpt) cc_final: 0.8451 (tpp) REVERT: B 628 TRP cc_start: 0.8337 (m100) cc_final: 0.7138 (m100) REVERT: B 647 GLU cc_start: 0.8961 (pp20) cc_final: 0.8520 (pp20) REVERT: B 655 LYS cc_start: 0.9069 (mttt) cc_final: 0.8825 (tptp) REVERT: E 37 THR cc_start: 0.9049 (m) cc_final: 0.8521 (p) REVERT: E 80 ASN cc_start: 0.8782 (t0) cc_final: 0.8257 (p0) REVERT: E 217 TYR cc_start: 0.9313 (m-80) cc_final: 0.8798 (m-10) REVERT: E 381 GLU cc_start: 0.8268 (mt-10) cc_final: 0.8046 (mt-10) REVERT: E 426 MET cc_start: 0.8598 (tpp) cc_final: 0.8296 (tpp) REVERT: E 434 MET cc_start: 0.8716 (tmm) cc_final: 0.8407 (tmm) REVERT: E 474 ASP cc_start: 0.8762 (t0) cc_final: 0.8481 (t0) REVERT: E 492 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8729 (mp0) REVERT: E 502 LYS cc_start: 0.9086 (tmmt) cc_final: 0.8832 (tptm) REVERT: F 536 THR cc_start: 0.9087 (p) cc_final: 0.8827 (t) REVERT: F 621 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7730 (mt-10) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.2666 time to fit residues: 97.7903 Evaluate side-chains 201 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN A 137 ASN A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 15737 Z= 0.313 Angle : 0.700 9.325 21401 Z= 0.350 Chirality : 0.047 0.504 2710 Planarity : 0.004 0.043 2630 Dihedral : 7.776 73.923 3688 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.07 % Allowed : 1.34 % Favored : 98.59 % 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: -0.77 (0.21), residues: 1635 helix: 0.07 (0.27), residues: 377 sheet: -0.02 (0.25), residues: 451 loop : -1.03 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP F 610 HIS 0.005 0.001 HIS E 105 PHE 0.016 0.002 PHE A 361 TYR 0.023 0.002 TYR A 39 ARG 0.010 0.001 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 239 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.9427 (m-30) cc_final: 0.9030 (m-30) REVERT: C 217 TYR cc_start: 0.9108 (m-80) cc_final: 0.8778 (m-80) REVERT: C 446 VAL cc_start: 0.8962 (t) cc_final: 0.8721 (t) REVERT: D 522 PHE cc_start: 0.8853 (t80) cc_final: 0.8331 (t80) REVERT: D 584 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8918 (tm-30) REVERT: D 585 ARG cc_start: 0.9385 (tpp80) cc_final: 0.9122 (tpp80) REVERT: D 593 LEU cc_start: 0.9643 (mt) cc_final: 0.9434 (tp) REVERT: D 596 TRP cc_start: 0.9222 (m-10) cc_final: 0.8287 (m-90) REVERT: D 648 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9080 (tm-30) REVERT: D 652 GLN cc_start: 0.9378 (mm110) cc_final: 0.8907 (mm110) REVERT: A 38 VAL cc_start: 0.9255 (t) cc_final: 0.9046 (p) REVERT: A 95 MET cc_start: 0.9318 (ptm) cc_final: 0.8174 (ppp) REVERT: A 211 GLU cc_start: 0.9266 (pp20) cc_final: 0.8866 (pm20) REVERT: A 377 ASN cc_start: 0.9127 (t0) cc_final: 0.8860 (t0) REVERT: A 381 GLU cc_start: 0.9146 (tp30) cc_final: 0.8498 (tp30) REVERT: B 530 MET cc_start: 0.8260 (mtm) cc_final: 0.6914 (mtt) REVERT: B 538 THR cc_start: 0.9442 (p) cc_final: 0.9195 (p) REVERT: B 577 GLN cc_start: 0.9025 (tm-30) cc_final: 0.8764 (tm-30) REVERT: B 628 TRP cc_start: 0.8338 (m100) cc_final: 0.7179 (m100) REVERT: B 647 GLU cc_start: 0.8988 (pp20) cc_final: 0.8540 (pp20) REVERT: B 655 LYS cc_start: 0.9056 (mttt) cc_final: 0.8803 (tptp) REVERT: E 80 ASN cc_start: 0.8892 (t0) cc_final: 0.8349 (p0) REVERT: E 155 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8179 (mmmt) REVERT: E 217 TYR cc_start: 0.9233 (m-80) cc_final: 0.8861 (m-10) REVERT: E 426 MET cc_start: 0.8637 (tpp) cc_final: 0.8191 (tpp) REVERT: E 434 MET cc_start: 0.8792 (tmm) cc_final: 0.8449 (tmm) REVERT: E 474 ASP cc_start: 0.8855 (t0) cc_final: 0.8550 (t0) REVERT: E 492 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8693 (mp0) REVERT: E 502 LYS cc_start: 0.9069 (tmmt) cc_final: 0.8788 (tptm) REVERT: F 536 THR cc_start: 0.9103 (p) cc_final: 0.8846 (t) REVERT: F 621 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7838 (mt-10) outliers start: 1 outliers final: 0 residues processed: 240 average time/residue: 0.2958 time to fit residues: 104.1094 Evaluate side-chains 193 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN D 625 ASN A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15737 Z= 0.323 Angle : 0.702 8.947 21401 Z= 0.355 Chirality : 0.047 0.504 2710 Planarity : 0.004 0.040 2630 Dihedral : 7.887 72.420 3688 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.07 % Allowed : 1.34 % Favored : 98.59 % 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: -1.01 (0.20), residues: 1635 helix: -0.07 (0.26), residues: 385 sheet: -0.12 (0.25), residues: 454 loop : -1.27 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP F 610 HIS 0.005 0.001 HIS A 105 PHE 0.017 0.002 PHE A 361 TYR 0.020 0.002 TYR A 39 ARG 0.006 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ASP cc_start: 0.9401 (m-30) cc_final: 0.9028 (m-30) REVERT: C 112 TRP cc_start: 0.8963 (t-100) cc_final: 0.8579 (t-100) REVERT: D 522 PHE cc_start: 0.8889 (t80) cc_final: 0.8507 (t80) REVERT: D 584 GLU cc_start: 0.9362 (mt-10) cc_final: 0.8913 (tm-30) REVERT: D 585 ARG cc_start: 0.9413 (tpp80) cc_final: 0.9153 (tpp80) REVERT: D 648 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8706 (tm-30) REVERT: D 652 GLN cc_start: 0.9283 (mm110) cc_final: 0.8876 (mm-40) REVERT: D 655 LYS cc_start: 0.9297 (pttt) cc_final: 0.9045 (pttp) REVERT: D 657 GLU cc_start: 0.9422 (mp0) cc_final: 0.9205 (mp0) REVERT: A 95 MET cc_start: 0.9308 (ptm) cc_final: 0.8303 (ppp) REVERT: A 211 GLU cc_start: 0.9265 (pp20) cc_final: 0.8917 (pm20) REVERT: A 377 ASN cc_start: 0.9145 (t0) cc_final: 0.8872 (t0) REVERT: A 381 GLU cc_start: 0.9136 (tp30) cc_final: 0.8477 (tp30) REVERT: B 530 MET cc_start: 0.8155 (mtm) cc_final: 0.7885 (mtp) REVERT: B 538 THR cc_start: 0.9447 (p) cc_final: 0.8922 (p) REVERT: B 577 GLN cc_start: 0.8988 (tm-30) cc_final: 0.8731 (tm-30) REVERT: B 626 MET cc_start: 0.8497 (tpt) cc_final: 0.8296 (tpp) REVERT: B 647 GLU cc_start: 0.9011 (pp20) cc_final: 0.8569 (pp20) REVERT: B 654 GLU cc_start: 0.9037 (tp30) cc_final: 0.8752 (tp30) REVERT: B 655 LYS cc_start: 0.9071 (mttt) cc_final: 0.8822 (tptp) REVERT: E 80 ASN cc_start: 0.8916 (t0) cc_final: 0.8321 (p0) REVERT: E 376 PHE cc_start: 0.8821 (t80) cc_final: 0.8618 (t80) REVERT: E 434 MET cc_start: 0.8805 (tmm) cc_final: 0.8478 (tmm) REVERT: E 474 ASP cc_start: 0.8851 (t0) cc_final: 0.8614 (t0) REVERT: E 492 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8644 (mp0) REVERT: E 502 LYS cc_start: 0.9032 (tmmt) cc_final: 0.8739 (tptm) REVERT: F 536 THR cc_start: 0.9167 (p) cc_final: 0.8896 (t) REVERT: F 621 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7847 (mt-10) outliers start: 1 outliers final: 1 residues processed: 239 average time/residue: 0.2743 time to fit residues: 96.8144 Evaluate side-chains 194 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 30.0000 chunk 156 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 20.0000 overall best weight: 1.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15737 Z= 0.191 Angle : 0.619 9.468 21401 Z= 0.313 Chirality : 0.046 0.490 2710 Planarity : 0.004 0.040 2630 Dihedral : 7.316 70.010 3688 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.83 (0.21), residues: 1635 helix: 0.04 (0.27), residues: 384 sheet: -0.12 (0.24), residues: 459 loop : -1.05 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP F 610 HIS 0.005 0.001 HIS A 249 PHE 0.019 0.002 PHE C 176 TYR 0.019 0.001 TYR A 39 ARG 0.006 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.9040 (ptp) cc_final: 0.8503 (ptp) REVERT: C 100 MET cc_start: 0.9277 (mmm) cc_final: 0.8979 (tpt) REVERT: C 107 ASP cc_start: 0.9294 (m-30) cc_final: 0.8975 (m-30) REVERT: C 426 MET cc_start: 0.8276 (ttm) cc_final: 0.7632 (ttm) REVERT: D 522 PHE cc_start: 0.8883 (t80) cc_final: 0.8433 (t80) REVERT: D 543 ASN cc_start: 0.8482 (m110) cc_final: 0.8278 (m-40) REVERT: D 584 GLU cc_start: 0.9341 (mt-10) cc_final: 0.8880 (tm-30) REVERT: D 585 ARG cc_start: 0.9434 (tpp80) cc_final: 0.9183 (tpp80) REVERT: D 596 TRP cc_start: 0.9149 (m-10) cc_final: 0.8658 (m-10) REVERT: D 648 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8763 (tm-30) REVERT: D 652 GLN cc_start: 0.9294 (mm110) cc_final: 0.8822 (mm-40) REVERT: D 655 LYS cc_start: 0.9264 (pttt) cc_final: 0.9016 (pttm) REVERT: A 95 MET cc_start: 0.9260 (ptm) cc_final: 0.8209 (ppp) REVERT: A 114 GLN cc_start: 0.9390 (tp40) cc_final: 0.8872 (tm-30) REVERT: A 150 MET cc_start: 0.8853 (mtm) cc_final: 0.8650 (ptp) REVERT: A 211 GLU cc_start: 0.9270 (pp20) cc_final: 0.8853 (pm20) REVERT: A 377 ASN cc_start: 0.9074 (t0) cc_final: 0.8813 (t0) REVERT: A 381 GLU cc_start: 0.9046 (tp30) cc_final: 0.8370 (tp30) REVERT: B 530 MET cc_start: 0.8360 (mtm) cc_final: 0.7630 (mtp) REVERT: B 538 THR cc_start: 0.9418 (p) cc_final: 0.9193 (p) REVERT: B 577 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8682 (tm-30) REVERT: B 628 TRP cc_start: 0.8345 (m100) cc_final: 0.8131 (m100) REVERT: B 647 GLU cc_start: 0.8999 (pp20) cc_final: 0.8514 (pp20) REVERT: B 655 LYS cc_start: 0.9056 (mttt) cc_final: 0.8805 (tptp) REVERT: E 37 THR cc_start: 0.8875 (m) cc_final: 0.8242 (p) REVERT: E 80 ASN cc_start: 0.8914 (t0) cc_final: 0.8328 (p0) REVERT: E 95 MET cc_start: 0.8503 (ppp) cc_final: 0.8255 (ppp) REVERT: E 155 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8148 (mmmt) REVERT: E 249 HIS cc_start: 0.9052 (p90) cc_final: 0.8613 (p90) REVERT: E 376 PHE cc_start: 0.8732 (t80) cc_final: 0.8510 (t80) REVERT: E 420 ILE cc_start: 0.9477 (mm) cc_final: 0.9247 (mm) REVERT: E 434 MET cc_start: 0.8782 (tmm) cc_final: 0.8421 (tmm) REVERT: E 492 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8638 (mp0) REVERT: F 536 THR cc_start: 0.9050 (p) cc_final: 0.8311 (t) REVERT: F 621 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7752 (mt-10) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2691 time to fit residues: 98.1885 Evaluate side-chains 198 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 652 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15737 Z= 0.348 Angle : 0.732 9.279 21401 Z= 0.369 Chirality : 0.047 0.502 2710 Planarity : 0.004 0.041 2630 Dihedral : 7.809 70.064 3688 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.73 % 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: -1.18 (0.20), residues: 1635 helix: -0.32 (0.26), residues: 379 sheet: -0.23 (0.24), residues: 452 loop : -1.29 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 35 HIS 0.007 0.001 HIS A 105 PHE 0.016 0.002 PHE A 361 TYR 0.021 0.002 TYR D 586 ARG 0.008 0.001 ARG B 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3270 Ramachandran restraints generated. 1635 Oldfield, 0 Emsley, 1635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.9152 (ptp) cc_final: 0.8845 (ptp) REVERT: C 107 ASP cc_start: 0.9288 (m-30) cc_final: 0.9029 (m-30) REVERT: C 285 LEU cc_start: 0.9567 (mp) cc_final: 0.9334 (tt) REVERT: D 522 PHE cc_start: 0.8885 (t80) cc_final: 0.8466 (t80) REVERT: D 543 ASN cc_start: 0.8644 (m110) cc_final: 0.8418 (m-40) REVERT: D 584 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8884 (tm-30) REVERT: D 585 ARG cc_start: 0.9389 (tpp80) cc_final: 0.9164 (tpp80) REVERT: D 648 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 652 GLN cc_start: 0.9281 (mm-40) cc_final: 0.8848 (mm-40) REVERT: A 95 MET cc_start: 0.9284 (ptm) cc_final: 0.8290 (ppp) REVERT: A 150 MET cc_start: 0.9048 (mtm) cc_final: 0.8813 (ptp) REVERT: A 211 GLU cc_start: 0.9301 (pp20) cc_final: 0.8884 (pm20) REVERT: A 377 ASN cc_start: 0.9174 (t0) cc_final: 0.8866 (t0) REVERT: A 381 GLU cc_start: 0.9120 (tp30) cc_final: 0.8480 (tp30) REVERT: B 530 MET cc_start: 0.8372 (mtm) cc_final: 0.7540 (mtp) REVERT: B 538 THR cc_start: 0.9452 (p) cc_final: 0.9112 (p) REVERT: B 577 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8714 (tm-30) REVERT: B 628 TRP cc_start: 0.8423 (m100) cc_final: 0.8108 (m100) REVERT: B 647 GLU cc_start: 0.9046 (pp20) cc_final: 0.8577 (pp20) REVERT: B 655 LYS cc_start: 0.9039 (mttt) cc_final: 0.8789 (tptp) REVERT: E 80 ASN cc_start: 0.8915 (t0) cc_final: 0.8278 (p0) REVERT: E 95 MET cc_start: 0.8706 (ppp) cc_final: 0.8382 (ppp) REVERT: E 211 GLU cc_start: 0.8992 (tt0) cc_final: 0.8663 (tm-30) REVERT: E 249 HIS cc_start: 0.9116 (p90) cc_final: 0.8586 (p90) REVERT: E 376 PHE cc_start: 0.8831 (t80) cc_final: 0.8623 (t80) REVERT: E 420 ILE cc_start: 0.9469 (mm) cc_final: 0.9238 (mm) REVERT: E 426 MET cc_start: 0.8708 (tpp) cc_final: 0.8394 (ttm) REVERT: E 492 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8558 (mp0) REVERT: F 536 THR cc_start: 0.8959 (p) cc_final: 0.8629 (t) REVERT: F 647 GLU cc_start: 0.8994 (pp20) cc_final: 0.8667 (pp20) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2614 time to fit residues: 88.9892 Evaluate side-chains 184 residues out of total 1492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.066293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.056675 restraints weight = 78002.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.058273 restraints weight = 46059.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.059397 restraints weight = 31519.972| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.6248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15737 Z= 0.164 Angle : 0.622 9.976 21401 Z= 0.313 Chirality : 0.046 0.484 2710 Planarity : 0.004 0.038 2630 Dihedral : 7.079 66.423 3688 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.07 % Allowed : 0.34 % Favored : 99.60 % 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: -0.85 (0.21), residues: 1635 helix: -0.07 (0.27), residues: 383 sheet: -0.14 (0.24), residues: 462 loop : -1.00 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 610 HIS 0.005 0.001 HIS A 249 PHE 0.023 0.002 PHE D 522 TYR 0.019 0.001 TYR A 39 ARG 0.008 0.000 ARG B 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2996.79 seconds wall clock time: 55 minutes 29.82 seconds (3329.82 seconds total)