Starting phenix.real_space_refine on Tue Dec 12 19:06:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/12_2023/7d4q_30576.pdb" } resolution = 2.74 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= 0.162 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 Cl 8 4.86 5 C 14672 2.51 5 N 3596 2.21 5 O 3980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B GLU 740": "OE1" <-> "OE2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 175": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 175": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D GLU 740": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22388 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 643} Chain breaks: 5 Chain: "B" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 643} Chain breaks: 5 Chain: "C" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 643} Chain breaks: 5 Chain: "D" Number of atoms: 5443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5443 Classifications: {'peptide': 668} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 643} Chain breaks: 5 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CA': 1, ' ZN': 1, 'GWR': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CA': 1, ' ZN': 1, 'GWR': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CA': 1, ' ZN': 1, 'GWR': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {' CA': 1, ' ZN': 1, 'GWR': 1, 'POV': 1, 'PTY': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1155 SG CYS A 176 48.460 106.807 73.631 1.00159.66 S ATOM 1169 SG CYS A 178 49.650 109.652 75.896 1.00177.58 S ATOM 1191 SG CYS A 181 51.607 106.379 75.791 1.00186.60 S ATOM 6598 SG CYS B 176 106.807 84.543 73.632 1.00159.66 S ATOM 6612 SG CYS B 178 109.653 83.353 75.897 1.00177.58 S ATOM 6634 SG CYS B 181 106.380 81.396 75.792 1.00186.60 S ATOM 12041 SG CYS C 176 84.544 26.196 73.630 1.00159.66 S ATOM 12055 SG CYS C 178 83.354 23.350 75.895 1.00177.58 S ATOM 12077 SG CYS C 181 81.397 26.623 75.790 1.00186.60 S ATOM 17484 SG CYS D 176 26.197 48.459 73.629 1.00159.66 S ATOM 17498 SG CYS D 178 23.351 49.649 75.894 1.00177.58 S ATOM 17520 SG CYS D 181 26.624 51.606 75.790 1.00186.60 S Time building chain proxies: 11.87, per 1000 atoms: 0.53 Number of scatterers: 22388 At special positions: 0 Unit cell: (133.823, 133.823, 135.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 Cl 8 17.00 S 116 16.00 P 8 15.00 O 3980 8.00 N 3596 7.00 C 14672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.76 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " Number of angles added : 12 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 77.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.965A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 615 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 734 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 340 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 615 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 734 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.566A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 615 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 734 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.514A pdb=" N GLU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.833A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.992A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 427 through 433 removed outlier: 3.665A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.693A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.964A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.760A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.565A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 615 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 634 through 650 removed outlier: 3.644A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 734 Processing helix chain 'D' and resid 740 through 761 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL B 166 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 4.617A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL C 166 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 18 through 20 removed outlier: 4.618A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4284 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: 7.11 Time building geometry restraints manager: 10.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3520 1.31 - 1.44: 6148 1.44 - 1.56: 13024 1.56 - 1.69: 16 1.69 - 1.82: 196 Bond restraints: 22904 Sorted by residual: bond pdb=" C31 GWR A 806 " pdb=" C32 GWR A 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR B 806 " pdb=" C32 GWR B 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR C 806 " pdb=" C32 GWR C 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C31 GWR D 806 " pdb=" C32 GWR D 806 " ideal model delta sigma weight residual 1.387 1.534 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" C29 GWR B 806 " pdb=" C31 GWR B 806 " ideal model delta sigma weight residual 1.388 1.534 -0.146 2.00e-02 2.50e+03 5.35e+01 ... (remaining 22899 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.87: 624 106.87 - 113.65: 12855 113.65 - 120.43: 9017 120.43 - 127.21: 8228 127.21 - 133.99: 284 Bond angle restraints: 31008 Sorted by residual: angle pdb=" C ILE A 18 " pdb=" CA ILE A 18 " pdb=" CB ILE A 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE B 18 " pdb=" CA ILE B 18 " pdb=" CB ILE B 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE C 18 " pdb=" CA ILE C 18 " pdb=" CB ILE C 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" C ILE D 18 " pdb=" CA ILE D 18 " pdb=" CB ILE D 18 " ideal model delta sigma weight residual 110.52 106.28 4.24 1.11e+00 8.12e-01 1.46e+01 angle pdb=" CAM Y01 D 803 " pdb=" CAY Y01 D 803 " pdb=" OAW Y01 D 803 " ideal model delta sigma weight residual 111.19 122.40 -11.21 3.00e+00 1.11e-01 1.40e+01 ... (remaining 31003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13056 17.89 - 35.78: 628 35.78 - 53.68: 140 53.68 - 71.57: 48 71.57 - 89.46: 24 Dihedral angle restraints: 13896 sinusoidal: 5984 harmonic: 7912 Sorted by residual: dihedral pdb=" CB GLU A 56 " pdb=" CG GLU A 56 " pdb=" CD GLU A 56 " pdb=" OE1 GLU A 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.46 -89.46 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 56 " pdb=" CG GLU C 56 " pdb=" CD GLU C 56 " pdb=" OE1 GLU C 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU D 56 " pdb=" CG GLU D 56 " pdb=" CD GLU D 56 " pdb=" OE1 GLU D 56 " ideal model delta sinusoidal sigma weight residual 0.00 89.44 -89.44 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 13893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3095 0.062 - 0.123: 324 0.123 - 0.185: 29 0.185 - 0.247: 8 0.247 - 0.308: 8 Chirality restraints: 3464 Sorted by residual: chirality pdb=" CA ILE C 18 " pdb=" N ILE C 18 " pdb=" C ILE C 18 " pdb=" CB ILE C 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ILE D 18 " pdb=" N ILE D 18 " pdb=" C ILE D 18 " pdb=" CB ILE D 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3461 not shown) Planarity restraints: 3804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 611 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 611 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 611 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 612 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 611 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ILE B 611 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE B 611 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 612 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 611 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ILE D 611 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE D 611 " 0.015 2.00e-02 2.50e+03 pdb=" N SER D 612 " 0.013 2.00e-02 2.50e+03 ... (remaining 3801 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4689 2.78 - 3.31: 22015 3.31 - 3.84: 37866 3.84 - 4.37: 44746 4.37 - 4.90: 76469 Nonbonded interactions: 185785 Sorted by model distance: nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.254 2.440 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.254 2.440 nonbonded pdb=" NE2 GLN C 573 " pdb=" O06 GWR C 806 " model vdw 2.288 2.520 ... (remaining 185780 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 2.300 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: 11.220 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 62.480 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.190 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 22904 Z= 0.553 Angle : 0.781 11.207 31008 Z= 0.365 Chirality : 0.042 0.308 3464 Planarity : 0.003 0.032 3804 Dihedral : 12.256 89.462 8732 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.67 % Allowed : 4.19 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.70 (0.16), residues: 2624 helix: 2.32 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : 0.28 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 315 HIS 0.002 0.001 HIS C 271 PHE 0.015 0.001 PHE A 341 TYR 0.015 0.001 TYR C 118 ARG 0.005 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 444 time to evaluate : 2.526 Fit side-chains outliers start: 16 outliers final: 0 residues processed: 460 average time/residue: 1.3839 time to fit residues: 720.4686 Evaluate side-chains 304 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 629 GLN B 163 GLN B 629 GLN C 163 GLN C 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22904 Z= 0.259 Angle : 0.522 7.285 31008 Z= 0.266 Chirality : 0.038 0.158 3464 Planarity : 0.004 0.049 3804 Dihedral : 8.042 54.125 3472 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.84 % Allowed : 10.39 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.65 (0.16), residues: 2624 helix: 2.29 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.22 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.004 0.001 HIS A 92 PHE 0.017 0.002 PHE C 341 TYR 0.011 0.001 TYR A 524 ARG 0.007 0.001 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 324 time to evaluate : 2.695 Fit side-chains outliers start: 44 outliers final: 16 residues processed: 344 average time/residue: 1.3375 time to fit residues: 525.0902 Evaluate side-chains 323 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 307 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 12 average time/residue: 0.7219 time to fit residues: 14.1868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 0.0060 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 163 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 163 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN D 163 GLN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22904 Z= 0.200 Angle : 0.465 6.560 31008 Z= 0.239 Chirality : 0.036 0.152 3464 Planarity : 0.004 0.039 3804 Dihedral : 7.767 56.225 3472 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.76 % Allowed : 12.27 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.72 (0.16), residues: 2624 helix: 2.36 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 315 HIS 0.004 0.001 HIS C 92 PHE 0.017 0.001 PHE B 341 TYR 0.012 0.001 TYR D 524 ARG 0.007 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 2.456 Fit side-chains outliers start: 42 outliers final: 10 residues processed: 336 average time/residue: 1.3526 time to fit residues: 518.9981 Evaluate side-chains 311 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 301 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.6422 time to fit residues: 7.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 537 GLN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 92 HIS B 537 GLN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 92 HIS C 537 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 GLN D 92 HIS D 537 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22904 Z= 0.171 Angle : 0.453 6.773 31008 Z= 0.232 Chirality : 0.035 0.150 3464 Planarity : 0.003 0.039 3804 Dihedral : 7.598 54.235 3472 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.47 % Allowed : 12.35 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.82 (0.16), residues: 2624 helix: 2.45 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 315 HIS 0.004 0.001 HIS C 92 PHE 0.017 0.001 PHE C 341 TYR 0.012 0.001 TYR C 524 ARG 0.008 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 307 time to evaluate : 2.488 Fit side-chains outliers start: 59 outliers final: 20 residues processed: 342 average time/residue: 1.2833 time to fit residues: 503.5170 Evaluate side-chains 322 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 302 time to evaluate : 2.469 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 12 residues processed: 8 average time/residue: 1.0193 time to fit residues: 13.0632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 10.0000 chunk 144 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 629 GLN A 711 GLN B 92 HIS B 629 GLN B 711 GLN C 92 HIS C 629 GLN C 711 GLN D 92 HIS D 629 GLN D 711 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22904 Z= 0.187 Angle : 0.459 7.679 31008 Z= 0.236 Chirality : 0.035 0.149 3464 Planarity : 0.004 0.038 3804 Dihedral : 7.574 53.934 3472 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.22 % Allowed : 13.15 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.80 (0.16), residues: 2624 helix: 2.43 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 315 HIS 0.003 0.001 HIS D 92 PHE 0.017 0.001 PHE C 341 TYR 0.012 0.001 TYR B 524 ARG 0.008 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 2.578 Fit side-chains outliers start: 53 outliers final: 16 residues processed: 343 average time/residue: 1.3798 time to fit residues: 544.0074 Evaluate side-chains 321 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 305 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.5233 time to fit residues: 10.0206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS B 92 HIS B 551 ASN B 711 GLN C 92 HIS D 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22904 Z= 0.198 Angle : 0.470 9.161 31008 Z= 0.242 Chirality : 0.036 0.149 3464 Planarity : 0.003 0.034 3804 Dihedral : 7.586 53.809 3472 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.26 % Allowed : 14.11 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.76 (0.16), residues: 2624 helix: 2.40 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.004 0.001 HIS A 92 PHE 0.017 0.001 PHE C 341 TYR 0.013 0.001 TYR D 524 ARG 0.007 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 317 time to evaluate : 2.356 Fit side-chains outliers start: 30 outliers final: 12 residues processed: 343 average time/residue: 1.3373 time to fit residues: 523.5678 Evaluate side-chains 310 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 298 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 3.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 551 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN B 92 HIS B 551 ASN ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 92 HIS C 551 ASN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 551 ASN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22904 Z= 0.171 Angle : 0.462 8.486 31008 Z= 0.239 Chirality : 0.036 0.179 3464 Planarity : 0.003 0.041 3804 Dihedral : 7.491 52.799 3472 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.30 % Allowed : 14.74 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.76 (0.16), residues: 2624 helix: 2.41 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 315 HIS 0.003 0.000 HIS B 92 PHE 0.017 0.001 PHE C 341 TYR 0.012 0.001 TYR A 524 ARG 0.009 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 312 time to evaluate : 2.479 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 329 average time/residue: 1.3294 time to fit residues: 501.6747 Evaluate side-chains 304 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 1.6497 time to fit residues: 9.1300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 173 optimal weight: 0.0020 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 551 ASN A 629 GLN A 711 GLN B 92 HIS B 551 ASN B 629 GLN B 711 GLN C 92 HIS C 551 ASN C 629 GLN C 711 GLN D 92 HIS D 551 ASN D 629 GLN D 711 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22904 Z= 0.168 Angle : 0.469 8.114 31008 Z= 0.244 Chirality : 0.036 0.207 3464 Planarity : 0.003 0.039 3804 Dihedral : 7.431 52.765 3472 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.76 (0.16), residues: 2624 helix: 2.41 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.10 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.004 0.000 HIS C 92 PHE 0.017 0.001 PHE A 341 TYR 0.011 0.001 TYR A 524 ARG 0.009 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 304 time to evaluate : 2.368 Fit side-chains outliers start: 48 outliers final: 15 residues processed: 336 average time/residue: 1.2955 time to fit residues: 501.0920 Evaluate side-chains 317 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 302 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 1.6205 time to fit residues: 10.5560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 0.5980 chunk 237 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 92 HIS A 551 ASN A 552 ASN B 38 ASN B 92 HIS B 551 ASN B 552 ASN B 626 ASN C 92 HIS C 551 ASN C 552 ASN D 92 HIS D 551 ASN D 552 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22904 Z= 0.173 Angle : 0.483 7.830 31008 Z= 0.253 Chirality : 0.037 0.229 3464 Planarity : 0.003 0.037 3804 Dihedral : 7.404 52.970 3472 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.47 % Allowed : 14.74 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.74 (0.16), residues: 2624 helix: 2.39 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.12 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.004 0.001 HIS A 92 PHE 0.012 0.001 PHE B 341 TYR 0.011 0.001 TYR A 524 ARG 0.009 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 308 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 8 residues processed: 331 average time/residue: 1.2553 time to fit residues: 481.1938 Evaluate side-chains 311 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 303 time to evaluate : 2.728 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 3.6971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 551 ASN A 629 GLN B 92 HIS B 551 ASN B 629 GLN C 92 HIS C 551 ASN C 629 GLN D 92 HIS D 551 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22904 Z= 0.168 Angle : 0.489 9.327 31008 Z= 0.256 Chirality : 0.036 0.220 3464 Planarity : 0.003 0.038 3804 Dihedral : 7.359 53.004 3472 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.09 % Allowed : 14.91 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.69 (0.16), residues: 2624 helix: 2.32 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 315 HIS 0.004 0.000 HIS C 92 PHE 0.017 0.001 PHE B 341 TYR 0.010 0.001 TYR B 524 ARG 0.009 0.000 ARG A 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 315 time to evaluate : 2.542 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 332 average time/residue: 1.2935 time to fit residues: 494.5175 Evaluate side-chains 316 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 305 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.6615 time to fit residues: 9.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 184 optimal weight: 0.5980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS A 551 ASN A 629 GLN A 711 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 551 ASN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 551 ASN C 711 GLN D 92 HIS D 551 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129676 restraints weight = 20241.620| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.54 r_work: 0.3248 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22904 Z= 0.275 Angle : 0.563 10.222 31008 Z= 0.295 Chirality : 0.039 0.221 3464 Planarity : 0.004 0.037 3804 Dihedral : 7.712 53.003 3472 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.13 % Allowed : 15.12 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.27 (0.16), residues: 2624 helix: 2.02 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.02 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 315 HIS 0.004 0.001 HIS C 92 PHE 0.018 0.002 PHE C 520 TYR 0.014 0.001 TYR B 524 ARG 0.009 0.000 ARG B 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8514.99 seconds wall clock time: 151 minutes 37.33 seconds (9097.33 seconds total)