Starting phenix.real_space_refine on Sat Mar 16 19:43:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l90_23243/03_2024/7l90_23243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l90_23243/03_2024/7l90_23243.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/7l90_23243/03_2024/7l90_23243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l90_23243/03_2024/7l90_23243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l90_23243/03_2024/7l90_23243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l90_23243/03_2024/7l90_23243_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 9647 2.51 5 N 2630 2.21 5 O 3099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E GLU 290": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15480 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3434 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 4 Chain: "B" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "C" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3439 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 3 Chain: "D" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1018 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "E" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3448 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 20, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 465 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'TRANS': 92} Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'UNK:plan-1': 93} Unresolved non-hydrogen planarities: 93 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.07, per 1000 atoms: 0.59 Number of scatterers: 15480 At special positions: 0 Unit cell: (126.69, 123.6, 149.35, 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 3099 8.00 N 2630 7.00 C 9647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.07 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=2.15 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.07 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.07 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 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 ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 601 " - " ASN A 392 " " NAG A 602 " - " ASN A 339 " " NAG A 603 " - " ASN A 332 " " NAG A 604 " - " ASN A 448 " " NAG A 605 " - " ASN A 133 " " NAG A 606 " - " ASN A 137 " " NAG A 607 " - " ASN A 160 " " NAG A 608 " - " ASN A 197 " " NAG A 609 " - " ASN A 234 " " NAG A 610 " - " ASN A 88 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 355 " " NAG A 613 " - " ASN A 241 " " NAG A 614 " - " ASN A 276 " " NAG A 615 " - " ASN A 301 " " NAG A 616 " - " ASN A 295 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 241 " " NAG C 603 " - " ASN C 276 " " NAG C 604 " - " ASN C 392 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 332 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG C 613 " - " ASN C 355 " " NAG C 614 " - " ASN C 289 " " NAG C 615 " - " ASN C 88 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN B 611 " " NAG M 1 " - " ASN C 386 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 156 " " NAG P 1 " - " ASN E 386 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 156 " Time building additional restraints: 7.03 Conformation dependent library (CDL) restraints added in 2.7 seconds 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 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: 51 helices and 30 sheets defined 27.8% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 116 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 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 353 removed outlier: 4.173A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.306A 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 544 removed outlier: 4.653A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 removed outlier: 3.562A pdb=" N LEU B 566 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.040A pdb=" N TRP B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 623' Processing helix chain 'B' and resid 628 through 634 removed outlier: 3.527A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 661 removed outlier: 4.193A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 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 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' 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 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.507A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 545 removed outlier: 5.203A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 4.154A pdb=" N LYS D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.957A pdb=" N ILE D 573 " --> pdb=" O THR D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 660 removed outlier: 4.405A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) 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 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 335 through 353 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 378 through 380 No H-bonds generated for 'chain 'E' and resid 378 through 380' 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 480 Processing helix chain 'F' and resid 532 through 545 removed outlier: 5.047A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 541 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN F 543 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 545 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 565 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 619 through 621 No H-bonds generated for 'chain 'F' and resid 619 through 621' Processing helix chain 'F' and resid 628 through 661 removed outlier: 3.575A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= F, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.421A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.283A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 414 through 417 removed outlier: 6.922A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.263A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.512A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= M, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= P, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= Q, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= R, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.692A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.325A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.349A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.585A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= W, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= X, first strand: chain 'E' and resid 53 through 55 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: 6.654A 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: 6.189A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 374 through 376 removed outlier: 4.318A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 304 through 308 497 hydrogen bonds defined for protein. 1260 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: 5.06 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3970 1.33 - 1.47: 4762 1.47 - 1.62: 6867 1.62 - 1.76: 23 1.76 - 1.90: 122 Bond restraints: 15744 Sorted by residual: bond pdb=" NE ARG C 503 " pdb=" CZ ARG C 503 " ideal model delta sigma weight residual 1.326 1.426 -0.100 1.10e-02 8.26e+03 8.28e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.393 0.104 1.40e-02 5.10e+03 5.53e+01 bond pdb=" CB ILE C 396 " pdb=" CG1 ILE C 396 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" CB LEU F 663 " pdb=" CG LEU F 663 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" CB ILE E 396 " pdb=" CG1 ILE E 396 " ideal model delta sigma weight residual 1.530 1.648 -0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 15739 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.85: 261 104.85 - 112.21: 7960 112.21 - 119.57: 6106 119.57 - 126.94: 6828 126.94 - 134.30: 254 Bond angle restraints: 21409 Sorted by residual: angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.01e+00 9.80e-01 7.88e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.34 -8.78 1.02e+00 9.61e-01 7.40e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.80 -8.24 1.02e+00 9.61e-01 6.53e+01 angle pdb=" C LEU C 288 " pdb=" N ASN C 289 " pdb=" CA ASN C 289 " ideal model delta sigma weight residual 120.28 131.10 -10.82 1.34e+00 5.57e-01 6.52e+01 angle pdb=" N ILE B 622 " pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 110.53 118.01 -7.48 9.40e-01 1.13e+00 6.33e+01 ... (remaining 21404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.94: 10151 21.94 - 43.88: 215 43.88 - 65.83: 78 65.83 - 87.77: 34 87.77 - 109.71: 12 Dihedral angle restraints: 10490 sinusoidal: 5000 harmonic: 5490 Sorted by residual: dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.92 -65.92 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.20 -65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.01 -59.01 1 1.00e+01 1.00e-02 4.66e+01 ... (remaining 10487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1788 0.106 - 0.211: 589 0.211 - 0.317: 183 0.317 - 0.422: 104 0.422 - 0.528: 34 Chirality restraints: 2698 Sorted by residual: 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 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+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 1.34e+02 ... (remaining 2695 not shown) Planarity restraints: 2699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 613 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG E 613 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG E 613 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG E 613 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG E 613 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 602 " 0.341 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG C 602 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG C 602 " 0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C 602 " -0.524 2.00e-02 2.50e+03 pdb=" O7 NAG C 602 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.318 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG K 1 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.470 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.053 2.00e-02 2.50e+03 ... (remaining 2696 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4619 2.84 - 3.36: 14782 3.36 - 3.87: 25538 3.87 - 4.39: 29919 4.39 - 4.90: 46347 Nonbonded interactions: 121205 Sorted by model distance: nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.330 2.440 nonbonded pdb=" NH1 ARG E 503 " pdb=" OE1 GLN F 650 " model vdw 2.428 2.520 nonbonded pdb=" N UNK L 51 " pdb=" N UNK L 52 " model vdw 2.477 2.560 nonbonded pdb=" O UNK L 32 " pdb=" N UNK L 49 " model vdw 2.482 2.520 nonbonded pdb=" NZ LYS C 97 " pdb=" OE2 GLU C 275 " model vdw 2.484 2.520 ... (remaining 121200 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 33 through 57 or resid 66 through 503 or resid 601 through \ 615)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 141 or resid 152 through \ 503 or resid 601 through 615)) selection = (chain 'E' and (resid 33 through 141 or resid 152 through 503 or resid 601 throu \ gh 615)) } ncs_group { reference = (chain 'B' and (resid 521 through 661 or resid 701 through 702)) selection = chain 'D' selection = (chain 'F' and (resid 521 through 661 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 17 through 109) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 10.790 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.910 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 0.159 15744 Z= 1.308 Angle : 1.763 11.872 21409 Z= 1.139 Chirality : 0.141 0.528 2698 Planarity : 0.016 0.302 2637 Dihedral : 11.858 109.709 6817 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.06 % 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: 0.73 (0.19), residues: 1656 helix: -0.03 (0.23), residues: 418 sheet: 1.00 (0.24), residues: 413 loop : 0.68 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.008 TRP F 571 HIS 0.010 0.002 HIS A 216 PHE 0.032 0.006 PHE C 383 TYR 0.065 0.008 TYR A 191 ARG 0.009 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 1.492 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: A 35 TRP cc_start: 0.8501 (m100) cc_final: 0.8014 (m100) REVERT: A 50 THR cc_start: 0.8861 (t) cc_final: 0.8495 (t) REVERT: A 120 VAL cc_start: 0.9231 (t) cc_final: 0.8278 (t) REVERT: A 356 ASN cc_start: 0.7920 (t0) cc_final: 0.7564 (p0) REVERT: B 523 LEU cc_start: 0.8674 (mt) cc_final: 0.8278 (mt) REVERT: B 566 LEU cc_start: 0.8753 (mt) cc_final: 0.8526 (pp) REVERT: B 650 GLN cc_start: 0.8938 (tp40) cc_final: 0.8511 (tm-30) REVERT: C 46 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8927 (mmmt) REVERT: C 50 THR cc_start: 0.9398 (t) cc_final: 0.9137 (t) REVERT: C 80 ASN cc_start: 0.8765 (m-40) cc_final: 0.8403 (t0) REVERT: C 168 LYS cc_start: 0.8949 (mmtt) cc_final: 0.8520 (mtmt) REVERT: C 190 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8596 (mp0) REVERT: C 316 TRP cc_start: 0.8541 (m100) cc_final: 0.7837 (m100) REVERT: C 338 TRP cc_start: 0.9582 (t-100) cc_final: 0.9189 (t-100) REVERT: C 349 LEU cc_start: 0.9692 (mt) cc_final: 0.9476 (mt) REVERT: C 390 LEU cc_start: 0.9458 (tp) cc_final: 0.8739 (tp) REVERT: C 391 PHE cc_start: 0.8838 (m-80) cc_final: 0.8375 (m-10) REVERT: C 475 MET cc_start: 0.8871 (mmt) cc_final: 0.8654 (mmm) REVERT: D 537 LEU cc_start: 0.9366 (mt) cc_final: 0.8965 (mt) REVERT: D 538 THR cc_start: 0.9411 (p) cc_final: 0.9168 (t) REVERT: D 539 VAL cc_start: 0.9258 (t) cc_final: 0.8864 (t) REVERT: D 543 ASN cc_start: 0.8558 (m-40) cc_final: 0.8353 (m-40) REVERT: D 586 TYR cc_start: 0.9356 (t80) cc_final: 0.8728 (t80) REVERT: D 588 ARG cc_start: 0.8923 (ttp-170) cc_final: 0.8627 (ttp80) REVERT: D 596 TRP cc_start: 0.8849 (m-10) cc_final: 0.8195 (m-10) REVERT: E 72 HIS cc_start: 0.8933 (m-70) cc_final: 0.8637 (m-70) REVERT: E 95 MET cc_start: 0.9116 (ptt) cc_final: 0.8321 (ptm) REVERT: E 180 ASP cc_start: 0.8343 (m-30) cc_final: 0.7801 (m-30) REVERT: E 340 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9205 (mm-30) REVERT: E 381 GLU cc_start: 0.8924 (tp30) cc_final: 0.8433 (tp30) REVERT: E 423 ILE cc_start: 0.9669 (mt) cc_final: 0.9341 (mm) REVERT: E 452 LEU cc_start: 0.9261 (mp) cc_final: 0.8525 (mp) REVERT: E 489 VAL cc_start: 0.9106 (m) cc_final: 0.8904 (m) REVERT: E 490 LYS cc_start: 0.9430 (pttt) cc_final: 0.9098 (tptt) REVERT: E 491 ILE cc_start: 0.9391 (mm) cc_final: 0.9150 (mm) REVERT: E 492 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8451 (mp0) REVERT: F 567 LYS cc_start: 0.9200 (mttt) cc_final: 0.8948 (mmtm) REVERT: F 592 LEU cc_start: 0.9280 (mt) cc_final: 0.8933 (mt) REVERT: F 596 TRP cc_start: 0.8552 (m-10) cc_final: 0.8019 (m-10) REVERT: F 607 ASN cc_start: 0.8813 (m-40) cc_final: 0.8475 (p0) REVERT: F 650 GLN cc_start: 0.9000 (tp40) cc_final: 0.8323 (tm-30) REVERT: F 661 LEU cc_start: 0.8280 (tp) cc_final: 0.7616 (tp) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.2829 time to fit residues: 212.5565 Evaluate side-chains 265 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 564 HIS D 630 GLN D 653 GLN E 130 GLN E 352 HIS E 432 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15744 Z= 0.265 Angle : 0.792 12.033 21409 Z= 0.403 Chirality : 0.050 0.347 2698 Planarity : 0.005 0.062 2637 Dihedral : 8.658 74.702 3616 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.20 % Allowed : 2.72 % Favored : 97.08 % 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: 0.82 (0.20), residues: 1656 helix: 0.82 (0.26), residues: 393 sheet: 0.89 (0.24), residues: 435 loop : 0.36 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 623 HIS 0.006 0.001 HIS D 564 PHE 0.016 0.002 PHE A 353 TYR 0.024 0.002 TYR F 643 ARG 0.011 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 356 time to evaluate : 1.743 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: A 35 TRP cc_start: 0.8685 (m100) cc_final: 0.8013 (m100) REVERT: A 356 ASN cc_start: 0.8010 (t0) cc_final: 0.7502 (p0) REVERT: B 602 LEU cc_start: 0.8979 (mt) cc_final: 0.8694 (pt) REVERT: B 603 ILE cc_start: 0.8785 (mt) cc_final: 0.8496 (tt) REVERT: B 634 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8789 (tm-30) REVERT: B 638 TYR cc_start: 0.8299 (m-80) cc_final: 0.8083 (m-10) REVERT: B 650 GLN cc_start: 0.8964 (tp40) cc_final: 0.8411 (tm-30) REVERT: B 654 GLU cc_start: 0.8960 (tp30) cc_final: 0.8631 (tp30) REVERT: C 46 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8751 (mmmt) REVERT: C 95 MET cc_start: 0.9293 (ptt) cc_final: 0.8783 (ptt) REVERT: C 98 ASN cc_start: 0.8968 (t0) cc_final: 0.8734 (t0) REVERT: C 100 MET cc_start: 0.9196 (mtm) cc_final: 0.8989 (mtp) REVERT: C 168 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8586 (mtmt) REVERT: C 190 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8483 (mp0) REVERT: C 316 TRP cc_start: 0.8737 (m100) cc_final: 0.8204 (m100) REVERT: C 338 TRP cc_start: 0.9490 (t-100) cc_final: 0.9112 (t-100) REVERT: C 342 LEU cc_start: 0.9666 (mp) cc_final: 0.9353 (mt) REVERT: C 374 HIS cc_start: 0.9110 (t70) cc_final: 0.8739 (t70) REVERT: C 390 LEU cc_start: 0.9413 (tp) cc_final: 0.8663 (tp) REVERT: C 391 PHE cc_start: 0.8955 (m-80) cc_final: 0.8314 (m-10) REVERT: C 475 MET cc_start: 0.8819 (mmt) cc_final: 0.7863 (mmm) REVERT: C 477 ASP cc_start: 0.9579 (m-30) cc_final: 0.9182 (m-30) REVERT: C 479 TRP cc_start: 0.8394 (m-10) cc_final: 0.7970 (m-90) REVERT: D 536 THR cc_start: 0.9211 (p) cc_final: 0.8996 (p) REVERT: D 538 THR cc_start: 0.9362 (p) cc_final: 0.9057 (t) REVERT: D 579 ARG cc_start: 0.8611 (mtt180) cc_final: 0.7959 (mtp180) REVERT: D 585 ARG cc_start: 0.9027 (mtp-110) cc_final: 0.8792 (mtp-110) REVERT: D 588 ARG cc_start: 0.9005 (ttp-170) cc_final: 0.8502 (tmm-80) REVERT: D 595 ILE cc_start: 0.9594 (mm) cc_final: 0.9356 (tp) REVERT: D 596 TRP cc_start: 0.8404 (m-10) cc_final: 0.8010 (m-90) REVERT: D 603 ILE cc_start: 0.9064 (tt) cc_final: 0.8803 (mm) REVERT: E 33 ASN cc_start: 0.8555 (t0) cc_final: 0.8346 (t0) REVERT: E 72 HIS cc_start: 0.8844 (m-70) cc_final: 0.8109 (m-70) REVERT: E 95 MET cc_start: 0.8983 (ptt) cc_final: 0.8385 (ptm) REVERT: E 104 MET cc_start: 0.9350 (ttm) cc_final: 0.8821 (ttp) REVERT: E 180 ASP cc_start: 0.8422 (m-30) cc_final: 0.7905 (m-30) REVERT: E 489 VAL cc_start: 0.9062 (m) cc_final: 0.8683 (m) REVERT: E 490 LYS cc_start: 0.9254 (pttt) cc_final: 0.8985 (tptt) REVERT: E 492 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8517 (mp0) REVERT: F 567 LYS cc_start: 0.9333 (mttt) cc_final: 0.8993 (mmtm) REVERT: F 577 GLN cc_start: 0.9363 (tt0) cc_final: 0.8998 (tp40) REVERT: F 591 GLN cc_start: 0.8711 (tt0) cc_final: 0.8465 (tt0) REVERT: F 601 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8811 (mtpp) REVERT: F 602 LEU cc_start: 0.9555 (mt) cc_final: 0.9184 (mt) REVERT: F 647 GLU cc_start: 0.7724 (tt0) cc_final: 0.7512 (tt0) REVERT: F 650 GLN cc_start: 0.8853 (tp40) cc_final: 0.8323 (tm-30) REVERT: F 651 ASN cc_start: 0.9224 (t0) cc_final: 0.8976 (t0) outliers start: 3 outliers final: 1 residues processed: 359 average time/residue: 0.2856 time to fit residues: 148.0457 Evaluate side-chains 246 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 113 optimal weight: 0.0570 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 352 HIS E 432 GLN F 564 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15744 Z= 0.227 Angle : 0.671 9.110 21409 Z= 0.340 Chirality : 0.046 0.299 2698 Planarity : 0.004 0.042 2637 Dihedral : 7.312 53.800 3616 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.21 % 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: 1656 helix: 0.86 (0.27), residues: 400 sheet: 0.80 (0.24), residues: 440 loop : 0.16 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 427 HIS 0.007 0.001 HIS E 352 PHE 0.015 0.002 PHE E 376 TYR 0.019 0.002 TYR F 643 ARG 0.006 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 325 time to evaluate : 1.633 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: A 35 TRP cc_start: 0.8716 (m100) cc_final: 0.8391 (m100) REVERT: A 288 LEU cc_start: 0.9464 (mp) cc_final: 0.9239 (mp) REVERT: A 356 ASN cc_start: 0.8017 (t0) cc_final: 0.7421 (p0) REVERT: B 602 LEU cc_start: 0.8847 (mt) cc_final: 0.8538 (pt) REVERT: B 634 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 657 GLU cc_start: 0.8769 (tp30) cc_final: 0.8287 (tp30) REVERT: C 95 MET cc_start: 0.9238 (ptt) cc_final: 0.8995 (ptm) REVERT: C 98 ASN cc_start: 0.9019 (t0) cc_final: 0.8796 (t0) REVERT: C 168 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8612 (mtmt) REVERT: C 316 TRP cc_start: 0.8718 (m100) cc_final: 0.8388 (m100) REVERT: C 338 TRP cc_start: 0.9426 (t-100) cc_final: 0.9077 (t-100) REVERT: C 390 LEU cc_start: 0.9436 (tp) cc_final: 0.8724 (tp) REVERT: C 391 PHE cc_start: 0.9011 (m-80) cc_final: 0.8272 (m-10) REVERT: C 502 LYS cc_start: 0.9180 (ptpt) cc_final: 0.8754 (pptt) REVERT: D 537 LEU cc_start: 0.9176 (mt) cc_final: 0.8871 (mt) REVERT: D 538 THR cc_start: 0.9257 (p) cc_final: 0.8866 (t) REVERT: D 579 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8096 (mtp180) REVERT: D 588 ARG cc_start: 0.8981 (ttp-170) cc_final: 0.8306 (tmm-80) REVERT: D 596 TRP cc_start: 0.8526 (m-10) cc_final: 0.8087 (m-90) REVERT: D 650 GLN cc_start: 0.9607 (tp40) cc_final: 0.9372 (tt0) REVERT: E 33 ASN cc_start: 0.8647 (t0) cc_final: 0.8384 (t0) REVERT: E 72 HIS cc_start: 0.8779 (m-70) cc_final: 0.7918 (m-70) REVERT: E 95 MET cc_start: 0.8957 (ptt) cc_final: 0.8510 (ptm) REVERT: E 104 MET cc_start: 0.9399 (ttm) cc_final: 0.8819 (ttp) REVERT: E 180 ASP cc_start: 0.8339 (m-30) cc_final: 0.7967 (m-30) REVERT: E 288 LEU cc_start: 0.9279 (mt) cc_final: 0.9054 (mt) REVERT: E 490 LYS cc_start: 0.9248 (pttt) cc_final: 0.8984 (tptt) REVERT: E 492 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8568 (mp0) REVERT: F 567 LYS cc_start: 0.9332 (mttt) cc_final: 0.9019 (mmtm) REVERT: F 601 LYS cc_start: 0.9282 (mmpt) cc_final: 0.9064 (mttt) REVERT: F 633 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9019 (mttm) REVERT: F 654 GLU cc_start: 0.8763 (tm-30) cc_final: 0.7676 (tm-30) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.2768 time to fit residues: 130.8667 Evaluate side-chains 232 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 20.0000 chunk 177 optimal weight: 30.0000 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 352 HIS E 352 HIS E 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 15744 Z= 0.340 Angle : 0.737 15.381 21409 Z= 0.370 Chirality : 0.047 0.371 2698 Planarity : 0.004 0.046 2637 Dihedral : 7.007 59.917 3616 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.82 % 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: 0.24 (0.20), residues: 1656 helix: 0.58 (0.27), residues: 400 sheet: 0.56 (0.25), residues: 405 loop : -0.15 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 427 HIS 0.013 0.002 HIS E 374 PHE 0.023 0.002 PHE E 376 TYR 0.022 0.002 TYR D 586 ARG 0.007 0.001 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 284 time to evaluate : 1.554 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: A 35 TRP cc_start: 0.8785 (m100) cc_final: 0.8443 (m100) REVERT: A 475 MET cc_start: 0.8880 (mmm) cc_final: 0.6610 (mmm) REVERT: B 603 ILE cc_start: 0.8746 (mt) cc_final: 0.8346 (tp) REVERT: B 629 LEU cc_start: 0.9206 (tt) cc_final: 0.8964 (tp) REVERT: B 631 TRP cc_start: 0.9224 (t-100) cc_final: 0.8937 (t-100) REVERT: B 657 GLU cc_start: 0.8911 (tp30) cc_final: 0.8358 (tp30) REVERT: C 39 TYR cc_start: 0.7831 (m-10) cc_final: 0.7612 (m-80) REVERT: C 98 ASN cc_start: 0.9180 (t0) cc_final: 0.8946 (t0) REVERT: C 168 LYS cc_start: 0.9248 (mmtt) cc_final: 0.8847 (mtmt) REVERT: C 316 TRP cc_start: 0.8912 (m100) cc_final: 0.8606 (m100) REVERT: C 338 TRP cc_start: 0.9479 (t-100) cc_final: 0.9031 (t-100) REVERT: C 390 LEU cc_start: 0.9435 (tp) cc_final: 0.8958 (tp) REVERT: C 426 MET cc_start: 0.9418 (tpt) cc_final: 0.8665 (tpp) REVERT: D 538 THR cc_start: 0.9254 (p) cc_final: 0.8837 (t) REVERT: D 542 ARG cc_start: 0.8431 (ttp-110) cc_final: 0.8000 (ttp-110) REVERT: D 579 ARG cc_start: 0.8677 (mtt180) cc_final: 0.8217 (mtp180) REVERT: D 585 ARG cc_start: 0.9194 (mtp-110) cc_final: 0.8507 (ptm160) REVERT: D 588 ARG cc_start: 0.9007 (ttp-170) cc_final: 0.8419 (tmm-80) REVERT: D 595 ILE cc_start: 0.9609 (tp) cc_final: 0.9357 (tp) REVERT: D 596 TRP cc_start: 0.8557 (m-10) cc_final: 0.8342 (m-90) REVERT: E 33 ASN cc_start: 0.8748 (t0) cc_final: 0.8500 (t0) REVERT: E 80 ASN cc_start: 0.8922 (t0) cc_final: 0.8722 (t0) REVERT: E 95 MET cc_start: 0.8954 (ptt) cc_final: 0.8703 (ptm) REVERT: E 180 ASP cc_start: 0.8441 (m-30) cc_final: 0.8093 (m-30) REVERT: E 288 LEU cc_start: 0.9413 (mt) cc_final: 0.9189 (mt) REVERT: E 490 LYS cc_start: 0.9287 (pttt) cc_final: 0.9009 (ptpt) REVERT: E 492 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8692 (mp0) REVERT: F 567 LYS cc_start: 0.9428 (mttt) cc_final: 0.9082 (mmtm) REVERT: F 601 LYS cc_start: 0.9161 (mmpt) cc_final: 0.8825 (ttmt) REVERT: F 653 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8833 (tm-30) outliers start: 1 outliers final: 0 residues processed: 285 average time/residue: 0.2696 time to fit residues: 112.8425 Evaluate side-chains 211 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15744 Z= 0.192 Angle : 0.615 14.484 21409 Z= 0.314 Chirality : 0.045 0.278 2698 Planarity : 0.004 0.046 2637 Dihedral : 6.143 57.003 3616 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.20 % Allowed : 1.86 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1656 helix: 0.57 (0.26), residues: 414 sheet: 0.38 (0.25), residues: 410 loop : -0.13 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 614 HIS 0.005 0.001 HIS E 352 PHE 0.017 0.001 PHE D 522 TYR 0.035 0.002 TYR F 643 ARG 0.017 0.001 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 301 time to evaluate : 1.637 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: A 35 TRP cc_start: 0.8706 (m100) cc_final: 0.8454 (m100) REVERT: A 288 LEU cc_start: 0.9419 (mp) cc_final: 0.9196 (mp) REVERT: A 475 MET cc_start: 0.8620 (mmm) cc_final: 0.7511 (mmm) REVERT: B 601 LYS cc_start: 0.9372 (pttm) cc_final: 0.9083 (pttm) REVERT: B 629 LEU cc_start: 0.9237 (tt) cc_final: 0.9019 (tp) REVERT: B 631 TRP cc_start: 0.9195 (t-100) cc_final: 0.8905 (t-100) REVERT: C 40 TYR cc_start: 0.8217 (t80) cc_final: 0.7897 (t80) REVERT: C 46 LYS cc_start: 0.9093 (mmpt) cc_final: 0.8707 (mmmt) REVERT: C 95 MET cc_start: 0.8929 (ppp) cc_final: 0.8683 (ppp) REVERT: C 168 LYS cc_start: 0.9249 (mmtt) cc_final: 0.8837 (mtmt) REVERT: C 316 TRP cc_start: 0.8820 (m100) cc_final: 0.8396 (m100) REVERT: C 352 HIS cc_start: 0.8011 (m-70) cc_final: 0.7083 (m-70) REVERT: C 390 LEU cc_start: 0.9472 (tp) cc_final: 0.9056 (tp) REVERT: C 484 TYR cc_start: 0.8958 (p90) cc_final: 0.8750 (p90) REVERT: C 492 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8047 (mp0) REVERT: D 537 LEU cc_start: 0.9241 (mt) cc_final: 0.8989 (mt) REVERT: D 538 THR cc_start: 0.9137 (p) cc_final: 0.8759 (t) REVERT: D 542 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8034 (ttp-110) REVERT: D 579 ARG cc_start: 0.8564 (mtt180) cc_final: 0.8028 (mtp180) REVERT: D 585 ARG cc_start: 0.9151 (mtp-110) cc_final: 0.8553 (ptm160) REVERT: D 586 TYR cc_start: 0.8980 (t80) cc_final: 0.8289 (t80) REVERT: D 588 ARG cc_start: 0.8953 (ttp-170) cc_final: 0.8231 (tmm-80) REVERT: D 595 ILE cc_start: 0.9670 (tp) cc_final: 0.9412 (tp) REVERT: D 596 TRP cc_start: 0.8337 (m-10) cc_final: 0.8098 (m-90) REVERT: E 33 ASN cc_start: 0.8768 (t0) cc_final: 0.8551 (t0) REVERT: E 95 MET cc_start: 0.8880 (ptt) cc_final: 0.8333 (ppp) REVERT: E 97 LYS cc_start: 0.9527 (mtpp) cc_final: 0.9304 (mtpp) REVERT: E 180 ASP cc_start: 0.8262 (m-30) cc_final: 0.7710 (m-30) REVERT: E 288 LEU cc_start: 0.9327 (mt) cc_final: 0.9098 (mt) REVERT: E 490 LYS cc_start: 0.9324 (pttt) cc_final: 0.8980 (ptpt) REVERT: E 492 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8704 (mp0) REVERT: F 567 LYS cc_start: 0.9394 (mttt) cc_final: 0.9056 (mmtm) REVERT: F 577 GLN cc_start: 0.9290 (tt0) cc_final: 0.8988 (tp40) REVERT: F 635 ILE cc_start: 0.9007 (pt) cc_final: 0.8161 (pt) outliers start: 3 outliers final: 0 residues processed: 304 average time/residue: 0.2745 time to fit residues: 121.8774 Evaluate side-chains 211 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 147 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 352 HIS E 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15744 Z= 0.278 Angle : 0.671 13.733 21409 Z= 0.340 Chirality : 0.046 0.556 2698 Planarity : 0.004 0.049 2637 Dihedral : 6.589 59.072 3616 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 0.01 (0.20), residues: 1656 helix: 0.54 (0.26), residues: 410 sheet: 0.15 (0.25), residues: 418 loop : -0.23 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 427 HIS 0.015 0.002 HIS E 374 PHE 0.020 0.002 PHE E 376 TYR 0.022 0.002 TYR F 643 ARG 0.007 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.555 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: A 35 TRP cc_start: 0.8824 (m100) cc_final: 0.8496 (m100) REVERT: A 109 ILE cc_start: 0.9413 (tt) cc_final: 0.9007 (mt) REVERT: A 288 LEU cc_start: 0.9467 (mp) cc_final: 0.9243 (mp) REVERT: A 475 MET cc_start: 0.8677 (mmm) cc_final: 0.7838 (mmm) REVERT: C 40 TYR cc_start: 0.8303 (t80) cc_final: 0.7992 (t80) REVERT: C 46 LYS cc_start: 0.9128 (mmpt) cc_final: 0.8735 (mmmt) REVERT: C 86 LEU cc_start: 0.9287 (mt) cc_final: 0.9086 (mt) REVERT: C 95 MET cc_start: 0.9048 (ppp) cc_final: 0.8656 (ppp) REVERT: C 168 LYS cc_start: 0.9325 (mmtt) cc_final: 0.8932 (mtpt) REVERT: C 316 TRP cc_start: 0.8859 (m100) cc_final: 0.8539 (m100) REVERT: C 390 LEU cc_start: 0.9493 (tp) cc_final: 0.9038 (tp) REVERT: D 579 ARG cc_start: 0.8601 (mtt180) cc_final: 0.8025 (mtp180) REVERT: D 585 ARG cc_start: 0.9197 (mtp-110) cc_final: 0.8947 (mtp-110) REVERT: D 588 ARG cc_start: 0.9012 (ttp-170) cc_final: 0.8436 (tmm-80) REVERT: D 590 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8866 (mp10) REVERT: D 595 ILE cc_start: 0.9640 (tp) cc_final: 0.9370 (tp) REVERT: D 596 TRP cc_start: 0.8422 (m-10) cc_final: 0.8203 (m-90) REVERT: E 33 ASN cc_start: 0.8802 (t0) cc_final: 0.8569 (t0) REVERT: E 80 ASN cc_start: 0.8915 (t0) cc_final: 0.8626 (t0) REVERT: E 95 MET cc_start: 0.8922 (ptt) cc_final: 0.8665 (ppp) REVERT: E 180 ASP cc_start: 0.8400 (m-30) cc_final: 0.8011 (m-30) REVERT: E 288 LEU cc_start: 0.9378 (mt) cc_final: 0.9143 (mt) REVERT: E 490 LYS cc_start: 0.9351 (pttt) cc_final: 0.8964 (ptpt) REVERT: E 492 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8742 (mp0) REVERT: F 567 LYS cc_start: 0.9412 (mttt) cc_final: 0.9076 (mmtm) REVERT: F 577 GLN cc_start: 0.9275 (tt0) cc_final: 0.8992 (tp40) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2498 time to fit residues: 98.5681 Evaluate side-chains 197 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 15744 Z= 0.303 Angle : 0.685 14.724 21409 Z= 0.348 Chirality : 0.046 0.277 2698 Planarity : 0.004 0.049 2637 Dihedral : 6.683 58.331 3616 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1656 helix: 0.29 (0.26), residues: 406 sheet: -0.03 (0.24), residues: 409 loop : -0.33 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 427 HIS 0.008 0.002 HIS A 105 PHE 0.017 0.002 PHE E 391 TYR 0.036 0.002 TYR F 643 ARG 0.007 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 1.831 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: A 35 TRP cc_start: 0.8776 (m100) cc_final: 0.8438 (m100) REVERT: A 109 ILE cc_start: 0.9410 (tt) cc_final: 0.9045 (mt) REVERT: A 180 ASP cc_start: 0.8611 (m-30) cc_final: 0.8126 (m-30) REVERT: A 288 LEU cc_start: 0.9432 (mp) cc_final: 0.9228 (mp) REVERT: B 601 LYS cc_start: 0.9373 (pttm) cc_final: 0.9042 (pttm) REVERT: B 650 GLN cc_start: 0.8990 (tp40) cc_final: 0.8609 (tm-30) REVERT: B 654 GLU cc_start: 0.9268 (tp30) cc_final: 0.8447 (tp30) REVERT: C 40 TYR cc_start: 0.8327 (t80) cc_final: 0.8072 (t80) REVERT: C 95 MET cc_start: 0.9084 (ppp) cc_final: 0.8306 (ppp) REVERT: C 168 LYS cc_start: 0.9378 (mmtt) cc_final: 0.8994 (mtpt) REVERT: C 316 TRP cc_start: 0.8928 (m100) cc_final: 0.8596 (m100) REVERT: C 390 LEU cc_start: 0.9521 (tp) cc_final: 0.9101 (tp) REVERT: D 579 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8079 (mtp180) REVERT: D 585 ARG cc_start: 0.9239 (mtp-110) cc_final: 0.8764 (mmm-85) REVERT: D 588 ARG cc_start: 0.9052 (ttp-170) cc_final: 0.8462 (tmm-80) REVERT: D 590 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8886 (mp10) REVERT: D 595 ILE cc_start: 0.9611 (tp) cc_final: 0.9310 (tp) REVERT: D 596 TRP cc_start: 0.8520 (m-10) cc_final: 0.8151 (m-90) REVERT: E 33 ASN cc_start: 0.8801 (t0) cc_final: 0.8548 (t0) REVERT: E 72 HIS cc_start: 0.8906 (m-70) cc_final: 0.8033 (m-70) REVERT: E 80 ASN cc_start: 0.8972 (t0) cc_final: 0.8686 (t0) REVERT: E 180 ASP cc_start: 0.8459 (m-30) cc_final: 0.8170 (m-30) REVERT: E 195 ASN cc_start: 0.9360 (p0) cc_final: 0.9013 (t0) REVERT: E 490 LYS cc_start: 0.9348 (pttt) cc_final: 0.8927 (ptpt) REVERT: E 492 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8756 (mp0) REVERT: F 567 LYS cc_start: 0.9456 (mttt) cc_final: 0.9099 (mmtm) outliers start: 1 outliers final: 0 residues processed: 260 average time/residue: 0.2737 time to fit residues: 104.4419 Evaluate side-chains 189 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 105 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15744 Z= 0.224 Angle : 0.642 14.741 21409 Z= 0.324 Chirality : 0.045 0.315 2698 Planarity : 0.004 0.047 2637 Dihedral : 6.569 62.366 3616 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % 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: -0.28 (0.20), residues: 1656 helix: 0.35 (0.27), residues: 401 sheet: -0.15 (0.25), residues: 401 loop : -0.35 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 614 HIS 0.006 0.001 HIS E 352 PHE 0.022 0.002 PHE D 522 TYR 0.024 0.002 TYR C 484 ARG 0.007 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 1.716 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: A 35 TRP cc_start: 0.8753 (m100) cc_final: 0.8442 (m100) REVERT: A 104 MET cc_start: 0.9050 (tmm) cc_final: 0.8747 (tmm) REVERT: A 180 ASP cc_start: 0.8568 (m-30) cc_final: 0.8268 (m-30) REVERT: A 288 LEU cc_start: 0.9431 (mp) cc_final: 0.9207 (mp) REVERT: B 601 LYS cc_start: 0.9365 (pttm) cc_final: 0.8985 (pttt) REVERT: B 629 LEU cc_start: 0.9269 (tt) cc_final: 0.8957 (tp) REVERT: B 656 ASN cc_start: 0.8989 (m110) cc_final: 0.8701 (m110) REVERT: C 40 TYR cc_start: 0.8365 (t80) cc_final: 0.8131 (t80) REVERT: C 95 MET cc_start: 0.9017 (ppp) cc_final: 0.8476 (ppp) REVERT: C 168 LYS cc_start: 0.9383 (mmtt) cc_final: 0.8998 (mtpt) REVERT: C 316 TRP cc_start: 0.8876 (m100) cc_final: 0.8475 (m100) REVERT: C 390 LEU cc_start: 0.9533 (tp) cc_final: 0.9055 (tp) REVERT: C 479 TRP cc_start: 0.8755 (m-90) cc_final: 0.8407 (m-90) REVERT: C 492 GLU cc_start: 0.8166 (mp0) cc_final: 0.7946 (tm-30) REVERT: D 579 ARG cc_start: 0.8533 (mtt180) cc_final: 0.7950 (mtp180) REVERT: D 585 ARG cc_start: 0.9243 (mtp-110) cc_final: 0.8880 (mmm-85) REVERT: D 588 ARG cc_start: 0.9028 (ttp-170) cc_final: 0.8366 (tmm-80) REVERT: D 590 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8779 (mp10) REVERT: D 595 ILE cc_start: 0.9609 (tp) cc_final: 0.9299 (tp) REVERT: D 596 TRP cc_start: 0.8409 (m-10) cc_final: 0.8034 (m-90) REVERT: E 33 ASN cc_start: 0.8787 (t0) cc_final: 0.8523 (t0) REVERT: E 42 VAL cc_start: 0.9459 (t) cc_final: 0.9073 (p) REVERT: E 72 HIS cc_start: 0.8801 (m-70) cc_final: 0.8032 (m-70) REVERT: E 80 ASN cc_start: 0.9007 (t0) cc_final: 0.8745 (t0) REVERT: E 95 MET cc_start: 0.9321 (ppp) cc_final: 0.8538 (ppp) REVERT: E 97 LYS cc_start: 0.9526 (mtpp) cc_final: 0.9295 (mtpp) REVERT: E 180 ASP cc_start: 0.8428 (m-30) cc_final: 0.7987 (m-30) REVERT: E 195 ASN cc_start: 0.9345 (p0) cc_final: 0.9007 (t0) REVERT: E 475 MET cc_start: 0.8998 (mmp) cc_final: 0.8752 (mmm) REVERT: E 490 LYS cc_start: 0.9335 (pttt) cc_final: 0.9018 (ptmt) REVERT: E 492 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8687 (mp0) REVERT: F 567 LYS cc_start: 0.9442 (mttt) cc_final: 0.9081 (mmtm) REVERT: F 652 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8016 (tp-100) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.2840 time to fit residues: 113.4077 Evaluate side-chains 193 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 30.0000 chunk 155 optimal weight: 0.2980 chunk 165 optimal weight: 30.0000 chunk 99 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 203 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15744 Z= 0.214 Angle : 0.629 14.547 21409 Z= 0.316 Chirality : 0.045 0.335 2698 Planarity : 0.004 0.050 2637 Dihedral : 6.392 73.447 3616 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.13 % Allowed : 0.53 % Favored : 99.34 % 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: -0.27 (0.20), residues: 1656 helix: 0.48 (0.27), residues: 401 sheet: -0.19 (0.24), residues: 416 loop : -0.39 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 614 HIS 0.005 0.001 HIS E 352 PHE 0.012 0.001 PHE E 376 TYR 0.024 0.002 TYR C 484 ARG 0.007 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 267 time to evaluate : 1.589 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: A 35 TRP cc_start: 0.8748 (m100) cc_final: 0.8405 (m100) REVERT: A 104 MET cc_start: 0.9059 (tmm) cc_final: 0.8589 (tmm) REVERT: A 180 ASP cc_start: 0.8542 (m-30) cc_final: 0.8278 (m-30) REVERT: A 288 LEU cc_start: 0.9445 (mp) cc_final: 0.9232 (mp) REVERT: B 601 LYS cc_start: 0.9347 (pttm) cc_final: 0.9111 (pttm) REVERT: C 80 ASN cc_start: 0.9110 (t0) cc_final: 0.8881 (t0) REVERT: C 95 MET cc_start: 0.9059 (ppp) cc_final: 0.8495 (ppp) REVERT: C 168 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8975 (mtpt) REVERT: C 203 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.8968 (pp30) REVERT: C 316 TRP cc_start: 0.8837 (m100) cc_final: 0.8386 (m100) REVERT: C 390 LEU cc_start: 0.9536 (tp) cc_final: 0.9114 (tp) REVERT: C 479 TRP cc_start: 0.8737 (m-90) cc_final: 0.8279 (m-90) REVERT: D 579 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8070 (ttp-170) REVERT: D 585 ARG cc_start: 0.9244 (mtp-110) cc_final: 0.8787 (mmm-85) REVERT: D 588 ARG cc_start: 0.9018 (ttp-170) cc_final: 0.8394 (tmm-80) REVERT: D 595 ILE cc_start: 0.9618 (tp) cc_final: 0.8967 (tp) REVERT: D 647 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9063 (tp30) REVERT: E 33 ASN cc_start: 0.8791 (t0) cc_final: 0.8528 (t0) REVERT: E 42 VAL cc_start: 0.9446 (t) cc_final: 0.9052 (p) REVERT: E 72 HIS cc_start: 0.8812 (m-70) cc_final: 0.8036 (m-70) REVERT: E 80 ASN cc_start: 0.9003 (t0) cc_final: 0.8770 (t0) REVERT: E 180 ASP cc_start: 0.8406 (m-30) cc_final: 0.7867 (m-30) REVERT: E 475 MET cc_start: 0.8923 (mmp) cc_final: 0.8555 (mmm) REVERT: E 490 LYS cc_start: 0.9344 (pttt) cc_final: 0.9034 (ptmt) REVERT: E 492 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8671 (mp0) REVERT: F 567 LYS cc_start: 0.9425 (mttt) cc_final: 0.9098 (mmtm) REVERT: F 652 GLN cc_start: 0.8629 (tp-100) cc_final: 0.7859 (tp-100) REVERT: F 656 ASN cc_start: 0.9155 (m-40) cc_final: 0.8807 (m110) outliers start: 2 outliers final: 0 residues processed: 269 average time/residue: 0.2651 time to fit residues: 105.1185 Evaluate side-chains 200 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 30.0000 chunk 168 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15744 Z= 0.230 Angle : 0.637 14.458 21409 Z= 0.321 Chirality : 0.045 0.264 2698 Planarity : 0.004 0.050 2637 Dihedral : 6.382 75.132 3616 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.07 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1656 helix: 0.43 (0.27), residues: 409 sheet: -0.15 (0.24), residues: 418 loop : -0.40 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 427 HIS 0.008 0.001 HIS E 374 PHE 0.021 0.001 PHE E 376 TYR 0.024 0.002 TYR C 484 ARG 0.007 0.000 ARG B 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3312 Ramachandran restraints generated. 1656 Oldfield, 0 Emsley, 1656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.774 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: A 35 TRP cc_start: 0.8722 (m100) cc_final: 0.8364 (m100) REVERT: A 45 TRP cc_start: 0.8164 (p90) cc_final: 0.7913 (p90) REVERT: A 180 ASP cc_start: 0.8558 (m-30) cc_final: 0.8298 (m-30) REVERT: A 288 LEU cc_start: 0.9429 (mp) cc_final: 0.9204 (mp) REVERT: B 601 LYS cc_start: 0.9369 (pttm) cc_final: 0.9163 (pttm) REVERT: B 634 GLU cc_start: 0.8524 (pp20) cc_final: 0.7943 (pp20) REVERT: B 635 ILE cc_start: 0.9424 (tp) cc_final: 0.9173 (tp) REVERT: B 638 TYR cc_start: 0.8833 (m-10) cc_final: 0.8596 (m-10) REVERT: C 80 ASN cc_start: 0.9087 (t0) cc_final: 0.8853 (t0) REVERT: C 95 MET cc_start: 0.9044 (ppp) cc_final: 0.8454 (ppp) REVERT: C 168 LYS cc_start: 0.9362 (mmtt) cc_final: 0.8969 (mtpt) REVERT: C 285 LEU cc_start: 0.9552 (mp) cc_final: 0.9322 (tp) REVERT: C 316 TRP cc_start: 0.8828 (m100) cc_final: 0.8335 (m100) REVERT: C 390 LEU cc_start: 0.9542 (tp) cc_final: 0.9117 (tp) REVERT: C 479 TRP cc_start: 0.8769 (m-90) cc_final: 0.8167 (m-90) REVERT: D 579 ARG cc_start: 0.8514 (mtt180) cc_final: 0.8110 (ttp-170) REVERT: D 585 ARG cc_start: 0.9279 (mtp-110) cc_final: 0.8794 (mmm-85) REVERT: D 588 ARG cc_start: 0.9027 (ttp-170) cc_final: 0.8368 (tmm-80) REVERT: D 628 TRP cc_start: 0.7398 (t-100) cc_final: 0.6926 (t-100) REVERT: E 33 ASN cc_start: 0.8818 (t0) cc_final: 0.8553 (t0) REVERT: E 42 VAL cc_start: 0.9442 (t) cc_final: 0.9060 (p) REVERT: E 72 HIS cc_start: 0.8800 (m-70) cc_final: 0.8004 (m-70) REVERT: E 180 ASP cc_start: 0.8436 (m-30) cc_final: 0.8066 (m-30) REVERT: E 490 LYS cc_start: 0.9356 (pttt) cc_final: 0.9028 (ptmt) REVERT: E 492 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8682 (mp0) REVERT: F 567 LYS cc_start: 0.9436 (mttt) cc_final: 0.9085 (mmtm) REVERT: F 596 TRP cc_start: 0.8400 (m-10) cc_final: 0.8047 (m-90) REVERT: F 631 TRP cc_start: 0.8662 (t-100) cc_final: 0.8403 (t-100) REVERT: F 635 ILE cc_start: 0.9116 (pt) cc_final: 0.8111 (pt) REVERT: F 652 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8017 (tp-100) REVERT: F 656 ASN cc_start: 0.9193 (m-40) cc_final: 0.8887 (m110) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.2744 time to fit residues: 105.0220 Evaluate side-chains 201 residues out of total 1508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS E 432 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.068852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056944 restraints weight = 77214.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.058506 restraints weight = 45779.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059576 restraints weight = 31435.452| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15744 Z= 0.190 Angle : 0.635 14.571 21409 Z= 0.319 Chirality : 0.045 0.266 2698 Planarity : 0.004 0.047 2637 Dihedral : 6.234 75.090 3616 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.07 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1656 helix: 0.36 (0.27), residues: 409 sheet: -0.13 (0.24), residues: 428 loop : -0.41 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 631 HIS 0.008 0.001 HIS E 374 PHE 0.011 0.001 PHE A 382 TYR 0.029 0.002 TYR F 643 ARG 0.007 0.000 ARG B 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.17 seconds wall clock time: 57 minutes 16.58 seconds (3436.58 seconds total)