Starting phenix.real_space_refine on Mon Mar 18 22:59:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/03_2024/7d4q_30576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/03_2024/7d4q_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_30576/03_2024/7d4q_30576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/03_2024/7d4q_30576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/03_2024/7d4q_30576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4q_30576/03_2024/7d4q_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.23, per 1000 atoms: 0.55 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: 9.48 Conformation dependent library (CDL) restraints added in 3.9 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: 2.34 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: 6.74 Time building geometry restraints manager: 9.95 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: 2.620 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: 11.430 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 63.620 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 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:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.640 ------------------------------------------------------------------------------- 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 : 2.655 Fit side-chains REVERT: A 38 ASN cc_start: 0.6211 (t0) cc_final: 0.5982 (t0) REVERT: A 41 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5870 (mt-10) REVERT: A 170 ARG cc_start: 0.6309 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: A 186 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5702 (mp0) REVERT: A 222 ARG cc_start: 0.6577 (ptp-170) cc_final: 0.5779 (mtm-85) REVERT: A 253 LYS cc_start: 0.5817 (tttt) cc_final: 0.5474 (ttpp) REVERT: A 257 ASP cc_start: 0.6826 (m-30) cc_final: 0.6275 (m-30) REVERT: A 272 ARG cc_start: 0.5758 (mtt180) cc_final: 0.4923 (mtt-85) REVERT: A 422 MET cc_start: 0.5880 (tpt) cc_final: 0.5508 (tpt) REVERT: A 442 MET cc_start: 0.4908 (mtp) cc_final: 0.4647 (mtp) REVERT: A 516 ASP cc_start: 0.5929 (m-30) cc_final: 0.5702 (t70) REVERT: A 551 ASN cc_start: 0.7500 (t0) cc_final: 0.7258 (t0) REVERT: A 617 LEU cc_start: 0.6508 (tp) cc_final: 0.6209 (mm) REVERT: A 636 ASP cc_start: 0.6520 (m-30) cc_final: 0.6304 (t70) REVERT: A 728 MET cc_start: 0.6136 (mmt) cc_final: 0.5772 (mmt) REVERT: A 745 GLU cc_start: 0.5297 (mt-10) cc_final: 0.5082 (mt-10) REVERT: A 760 LEU cc_start: 0.6479 (mm) cc_final: 0.6278 (mm) REVERT: B 38 ASN cc_start: 0.6209 (t0) cc_final: 0.5980 (t0) REVERT: B 41 GLU cc_start: 0.6092 (mt-10) cc_final: 0.5870 (mt-10) REVERT: B 170 ARG cc_start: 0.6308 (mtp180) cc_final: 0.5645 (ptp-170) REVERT: B 186 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5732 (mp0) REVERT: B 222 ARG cc_start: 0.6577 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: B 253 LYS cc_start: 0.5818 (tttt) cc_final: 0.5473 (ttpp) REVERT: B 257 ASP cc_start: 0.6824 (m-30) cc_final: 0.6272 (m-30) REVERT: B 272 ARG cc_start: 0.5725 (mtt180) cc_final: 0.4888 (mtt-85) REVERT: B 422 MET cc_start: 0.5879 (tpt) cc_final: 0.5506 (tpt) REVERT: B 442 MET cc_start: 0.4908 (mtp) cc_final: 0.4647 (mtp) REVERT: B 516 ASP cc_start: 0.5928 (m-30) cc_final: 0.5703 (t70) REVERT: B 551 ASN cc_start: 0.7500 (t0) cc_final: 0.7256 (t0) REVERT: B 617 LEU cc_start: 0.6509 (tp) cc_final: 0.6208 (mm) REVERT: B 636 ASP cc_start: 0.6538 (m-30) cc_final: 0.6301 (t70) REVERT: B 728 MET cc_start: 0.6149 (mmt) cc_final: 0.5787 (mmt) REVERT: B 745 GLU cc_start: 0.5296 (mt-10) cc_final: 0.5081 (mt-10) REVERT: B 760 LEU cc_start: 0.6478 (mm) cc_final: 0.6278 (mm) REVERT: C 38 ASN cc_start: 0.6210 (t0) cc_final: 0.5981 (t0) REVERT: C 41 GLU cc_start: 0.6076 (mt-10) cc_final: 0.5858 (mt-10) REVERT: C 170 ARG cc_start: 0.6311 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: C 186 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5644 (mp0) REVERT: C 222 ARG cc_start: 0.6578 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: C 253 LYS cc_start: 0.5815 (tttt) cc_final: 0.5467 (ttpp) REVERT: C 257 ASP cc_start: 0.6825 (m-30) cc_final: 0.6270 (m-30) REVERT: C 272 ARG cc_start: 0.5725 (mtt180) cc_final: 0.4888 (mtt-85) REVERT: C 422 MET cc_start: 0.5882 (tpt) cc_final: 0.5509 (tpt) REVERT: C 442 MET cc_start: 0.4910 (mtp) cc_final: 0.4649 (mtp) REVERT: C 516 ASP cc_start: 0.5928 (m-30) cc_final: 0.5704 (t70) REVERT: C 551 ASN cc_start: 0.7499 (t0) cc_final: 0.7256 (t0) REVERT: C 617 LEU cc_start: 0.6505 (tp) cc_final: 0.6203 (mm) REVERT: C 636 ASP cc_start: 0.6540 (m-30) cc_final: 0.6301 (t70) REVERT: C 728 MET cc_start: 0.6136 (mmt) cc_final: 0.5772 (mmt) REVERT: C 745 GLU cc_start: 0.5297 (mt-10) cc_final: 0.5082 (mt-10) REVERT: C 760 LEU cc_start: 0.6477 (mm) cc_final: 0.6276 (mm) REVERT: D 38 ASN cc_start: 0.6210 (t0) cc_final: 0.5980 (t0) REVERT: D 41 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5872 (mt-10) REVERT: D 170 ARG cc_start: 0.6311 (mtp180) cc_final: 0.5647 (ptp-170) REVERT: D 186 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5642 (mp0) REVERT: D 222 ARG cc_start: 0.6579 (ptp-170) cc_final: 0.5781 (mtm-85) REVERT: D 253 LYS cc_start: 0.5817 (tttt) cc_final: 0.5474 (ttpp) REVERT: D 257 ASP cc_start: 0.6830 (m-30) cc_final: 0.6280 (m-30) REVERT: D 272 ARG cc_start: 0.5762 (mtt180) cc_final: 0.4925 (mtt-85) REVERT: D 422 MET cc_start: 0.5882 (tpt) cc_final: 0.5509 (tpt) REVERT: D 442 MET cc_start: 0.4907 (mtp) cc_final: 0.4647 (mtp) REVERT: D 516 ASP cc_start: 0.5933 (m-30) cc_final: 0.5703 (t70) REVERT: D 551 ASN cc_start: 0.7508 (t0) cc_final: 0.7258 (t0) REVERT: D 617 LEU cc_start: 0.6503 (tp) cc_final: 0.6202 (mm) REVERT: D 636 ASP cc_start: 0.6537 (m-30) cc_final: 0.6296 (t70) REVERT: D 728 MET cc_start: 0.6135 (mmt) cc_final: 0.5772 (mmt) REVERT: D 745 GLU cc_start: 0.5299 (mt-10) cc_final: 0.5085 (mt-10) REVERT: D 760 LEU cc_start: 0.6476 (mm) cc_final: 0.6276 (mm) outliers start: 16 outliers final: 0 residues processed: 460 average time/residue: 1.3662 time to fit residues: 710.5862 Evaluate side-chains 320 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9990 chunk 125 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 552 ASN B 629 GLN C 163 GLN C 552 ASN C 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22904 Z= 0.198 Angle : 0.477 6.579 31008 Z= 0.242 Chirality : 0.036 0.155 3464 Planarity : 0.004 0.047 3804 Dihedral : 7.852 53.320 3472 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.01 % Allowed : 9.72 % Favored : 89.28 % 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: 2.84 (0.16), residues: 2624 helix: 2.42 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.004 0.001 HIS A 92 PHE 0.017 0.001 PHE C 341 TYR 0.009 0.001 TYR D 524 ARG 0.008 0.001 ARG C 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 361 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 2.596 Fit side-chains REVERT: A 38 ASN cc_start: 0.6315 (t0) cc_final: 0.6113 (t160) REVERT: A 41 GLU cc_start: 0.6231 (mt-10) cc_final: 0.5975 (mt-10) REVERT: A 170 ARG cc_start: 0.6532 (mtp180) cc_final: 0.5574 (ptt180) REVERT: A 186 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5679 (mp0) REVERT: A 222 ARG cc_start: 0.6593 (ptp-170) cc_final: 0.5790 (mtm-85) REVERT: A 253 LYS cc_start: 0.5973 (tmtt) cc_final: 0.5570 (ttpp) REVERT: A 257 ASP cc_start: 0.6781 (m-30) cc_final: 0.6169 (m-30) REVERT: A 272 ARG cc_start: 0.6069 (mtt180) cc_final: 0.5156 (mtt-85) REVERT: A 337 ILE cc_start: 0.5782 (mm) cc_final: 0.5575 (mp) REVERT: A 422 MET cc_start: 0.5675 (tpt) cc_final: 0.5320 (tpt) REVERT: A 516 ASP cc_start: 0.5871 (m-30) cc_final: 0.5662 (t70) REVERT: A 551 ASN cc_start: 0.7645 (t0) cc_final: 0.7296 (t0) REVERT: A 636 ASP cc_start: 0.6550 (m-30) cc_final: 0.6245 (t70) REVERT: A 728 MET cc_start: 0.6227 (mmt) cc_final: 0.5959 (mmt) REVERT: A 745 GLU cc_start: 0.5379 (mt-10) cc_final: 0.5153 (mt-10) REVERT: B 38 ASN cc_start: 0.6314 (t0) cc_final: 0.6113 (t160) REVERT: B 41 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5975 (mt-10) REVERT: B 170 ARG cc_start: 0.6533 (mtp180) cc_final: 0.5576 (ptt180) REVERT: B 186 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5684 (mp0) REVERT: B 222 ARG cc_start: 0.6596 (ptp-170) cc_final: 0.5792 (mtm-85) REVERT: B 253 LYS cc_start: 0.5971 (tmtt) cc_final: 0.5567 (ttpp) REVERT: B 257 ASP cc_start: 0.6810 (m-30) cc_final: 0.6189 (m-30) REVERT: B 272 ARG cc_start: 0.6034 (mtt180) cc_final: 0.5129 (mtt-85) REVERT: B 337 ILE cc_start: 0.5785 (mm) cc_final: 0.5578 (mp) REVERT: B 422 MET cc_start: 0.5675 (tpt) cc_final: 0.5319 (tpt) REVERT: B 516 ASP cc_start: 0.5870 (m-30) cc_final: 0.5663 (t70) REVERT: B 551 ASN cc_start: 0.7646 (t0) cc_final: 0.7295 (t0) REVERT: B 636 ASP cc_start: 0.6552 (m-30) cc_final: 0.6245 (t70) REVERT: B 728 MET cc_start: 0.6228 (mmt) cc_final: 0.5960 (mmt) REVERT: B 745 GLU cc_start: 0.5380 (mt-10) cc_final: 0.5152 (mt-10) REVERT: C 38 ASN cc_start: 0.6315 (t0) cc_final: 0.6115 (t160) REVERT: C 41 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5977 (mt-10) REVERT: C 170 ARG cc_start: 0.6535 (mtp180) cc_final: 0.5577 (ptt180) REVERT: C 186 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5689 (mp0) REVERT: C 222 ARG cc_start: 0.6588 (ptp-170) cc_final: 0.5789 (mtm-85) REVERT: C 253 LYS cc_start: 0.5971 (tmtt) cc_final: 0.5567 (ttpp) REVERT: C 257 ASP cc_start: 0.6810 (m-30) cc_final: 0.6188 (m-30) REVERT: C 272 ARG cc_start: 0.6035 (mtt180) cc_final: 0.5130 (mtt-85) REVERT: C 337 ILE cc_start: 0.5785 (mm) cc_final: 0.5579 (mp) REVERT: C 422 MET cc_start: 0.5677 (tpt) cc_final: 0.5320 (tpt) REVERT: C 516 ASP cc_start: 0.5869 (m-30) cc_final: 0.5662 (t70) REVERT: C 551 ASN cc_start: 0.7644 (t0) cc_final: 0.7295 (t0) REVERT: C 636 ASP cc_start: 0.6554 (m-30) cc_final: 0.6245 (t70) REVERT: C 728 MET cc_start: 0.6229 (mmt) cc_final: 0.5960 (mmt) REVERT: C 745 GLU cc_start: 0.5352 (mt-10) cc_final: 0.5124 (mt-10) REVERT: D 38 ASN cc_start: 0.6315 (t0) cc_final: 0.6115 (t160) REVERT: D 41 GLU cc_start: 0.6230 (mt-10) cc_final: 0.5975 (mt-10) REVERT: D 170 ARG cc_start: 0.6536 (mtp180) cc_final: 0.5577 (ptt180) REVERT: D 186 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5688 (mp0) REVERT: D 222 ARG cc_start: 0.6587 (ptp-170) cc_final: 0.5788 (mtm-85) REVERT: D 253 LYS cc_start: 0.5972 (tmtt) cc_final: 0.5569 (ttpp) REVERT: D 257 ASP cc_start: 0.6782 (m-30) cc_final: 0.6170 (m-30) REVERT: D 272 ARG cc_start: 0.6035 (mtt180) cc_final: 0.5130 (mtt-85) REVERT: D 337 ILE cc_start: 0.5785 (mm) cc_final: 0.5577 (mp) REVERT: D 422 MET cc_start: 0.5678 (tpt) cc_final: 0.5321 (tpt) REVERT: D 516 ASP cc_start: 0.5871 (m-30) cc_final: 0.5662 (t70) REVERT: D 551 ASN cc_start: 0.7645 (t0) cc_final: 0.7315 (t0) REVERT: D 636 ASP cc_start: 0.6551 (m-30) cc_final: 0.6244 (t70) REVERT: D 728 MET cc_start: 0.6227 (mmt) cc_final: 0.5960 (mmt) REVERT: D 745 GLU cc_start: 0.5375 (mt-10) cc_final: 0.5150 (mt-10) outliers start: 24 outliers final: 8 residues processed: 341 average time/residue: 1.4089 time to fit residues: 545.6197 Evaluate side-chains 327 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 319 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 652 ASP 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: 0.3980 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 chunk 240 optimal weight: 0.3980 chunk 259 optimal weight: 0.0000 chunk 213 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** D 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22904 Z= 0.116 Angle : 0.410 6.227 31008 Z= 0.209 Chirality : 0.034 0.151 3464 Planarity : 0.003 0.041 3804 Dihedral : 7.386 52.930 3472 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.17 % Allowed : 11.56 % Favored : 87.27 % 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: 3.14 (0.16), residues: 2624 helix: 2.66 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.29 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 315 HIS 0.003 0.000 HIS B 92 PHE 0.017 0.001 PHE B 341 TYR 0.009 0.001 TYR C 586 ARG 0.008 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 370 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 342 time to evaluate : 2.554 Fit side-chains REVERT: A 41 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5923 (mt-10) REVERT: A 170 ARG cc_start: 0.6651 (mtp180) cc_final: 0.5698 (ptt180) REVERT: A 186 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5605 (mp0) REVERT: A 222 ARG cc_start: 0.6559 (ptp-170) cc_final: 0.5777 (mtm-85) REVERT: A 253 LYS cc_start: 0.5818 (tttt) cc_final: 0.5602 (ttpp) REVERT: A 272 ARG cc_start: 0.5967 (mtt180) cc_final: 0.5084 (mtt-85) REVERT: A 337 ILE cc_start: 0.5765 (mm) cc_final: 0.5551 (mp) REVERT: A 422 MET cc_start: 0.5672 (tpt) cc_final: 0.5322 (tpt) REVERT: A 467 GLU cc_start: 0.7781 (mp0) cc_final: 0.7401 (pm20) REVERT: A 512 ARG cc_start: 0.6776 (mtm110) cc_final: 0.6452 (mtm110) REVERT: A 516 ASP cc_start: 0.5779 (m-30) cc_final: 0.5560 (t70) REVERT: A 551 ASN cc_start: 0.7497 (t0) cc_final: 0.7113 (t0) REVERT: A 636 ASP cc_start: 0.6465 (m-30) cc_final: 0.6167 (t70) REVERT: A 728 MET cc_start: 0.6201 (mmt) cc_final: 0.5780 (mmp) REVERT: A 745 GLU cc_start: 0.5440 (mt-10) cc_final: 0.5177 (mt-10) REVERT: B 41 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5655 (mm-30) REVERT: B 170 ARG cc_start: 0.6649 (mtp180) cc_final: 0.5697 (ptt180) REVERT: B 186 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5605 (mp0) REVERT: B 222 ARG cc_start: 0.6559 (ptp-170) cc_final: 0.5777 (mtm-85) REVERT: B 253 LYS cc_start: 0.5816 (tttt) cc_final: 0.5601 (ttpp) REVERT: B 272 ARG cc_start: 0.5979 (mtt180) cc_final: 0.5093 (mtt-85) REVERT: B 337 ILE cc_start: 0.5703 (mm) cc_final: 0.5492 (mp) REVERT: B 422 MET cc_start: 0.5671 (tpt) cc_final: 0.5322 (tpt) REVERT: B 467 GLU cc_start: 0.7797 (mp0) cc_final: 0.7420 (pm20) REVERT: B 512 ARG cc_start: 0.6783 (mtm110) cc_final: 0.6457 (mtm110) REVERT: B 551 ASN cc_start: 0.7547 (t0) cc_final: 0.7200 (t0) REVERT: B 636 ASP cc_start: 0.6466 (m-30) cc_final: 0.6167 (t70) REVERT: B 728 MET cc_start: 0.6202 (mmt) cc_final: 0.5780 (mmp) REVERT: B 745 GLU cc_start: 0.5445 (mt-10) cc_final: 0.5181 (mt-10) REVERT: C 41 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5924 (mt-10) REVERT: C 170 ARG cc_start: 0.6652 (mtp180) cc_final: 0.5698 (ptt180) REVERT: C 186 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5610 (mp0) REVERT: C 222 ARG cc_start: 0.6550 (ptp-170) cc_final: 0.5767 (mtm-85) REVERT: C 253 LYS cc_start: 0.5816 (tttt) cc_final: 0.5600 (ttpp) REVERT: C 272 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5085 (mtt-85) REVERT: C 337 ILE cc_start: 0.5768 (mm) cc_final: 0.5554 (mp) REVERT: C 422 MET cc_start: 0.5675 (tpt) cc_final: 0.5325 (tpt) REVERT: C 467 GLU cc_start: 0.7777 (mp0) cc_final: 0.7400 (pm20) REVERT: C 512 ARG cc_start: 0.6778 (mtm110) cc_final: 0.6455 (mtm110) REVERT: C 551 ASN cc_start: 0.7546 (t0) cc_final: 0.7204 (t0) REVERT: C 636 ASP cc_start: 0.6473 (m-30) cc_final: 0.6167 (t70) REVERT: C 728 MET cc_start: 0.6201 (mmt) cc_final: 0.5778 (mmp) REVERT: C 745 GLU cc_start: 0.5443 (mt-10) cc_final: 0.5180 (mt-10) REVERT: D 41 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5655 (mm-30) REVERT: D 170 ARG cc_start: 0.6651 (mtp180) cc_final: 0.5706 (ptt180) REVERT: D 186 GLU cc_start: 0.5900 (mt-10) cc_final: 0.5609 (mp0) REVERT: D 222 ARG cc_start: 0.6550 (ptp-170) cc_final: 0.5767 (mtm-85) REVERT: D 253 LYS cc_start: 0.5816 (tttt) cc_final: 0.5600 (ttpp) REVERT: D 272 ARG cc_start: 0.5965 (mtt180) cc_final: 0.5084 (mtt-85) REVERT: D 337 ILE cc_start: 0.5765 (mm) cc_final: 0.5552 (mp) REVERT: D 422 MET cc_start: 0.5677 (tpt) cc_final: 0.5327 (tpt) REVERT: D 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7400 (pm20) REVERT: D 512 ARG cc_start: 0.6770 (mtm110) cc_final: 0.6447 (mtm110) REVERT: D 516 ASP cc_start: 0.5777 (m-30) cc_final: 0.5567 (t70) REVERT: D 551 ASN cc_start: 0.7506 (t0) cc_final: 0.7118 (t0) REVERT: D 636 ASP cc_start: 0.6468 (m-30) cc_final: 0.6164 (t70) REVERT: D 728 MET cc_start: 0.6202 (mmt) cc_final: 0.5779 (mmp) REVERT: D 745 GLU cc_start: 0.5440 (mt-10) cc_final: 0.5178 (mt-10) outliers start: 28 outliers final: 12 residues processed: 350 average time/residue: 1.3478 time to fit residues: 536.3422 Evaluate side-chains 338 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 326 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 739 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 0.5980 chunk 255 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 GLN A 537 GLN A 629 GLN ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 443 ASN B 537 GLN B 629 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN C 443 ASN C 537 GLN C 629 GLN ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 537 GLN D 629 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22904 Z= 0.193 Angle : 0.452 7.213 31008 Z= 0.230 Chirality : 0.035 0.152 3464 Planarity : 0.004 0.044 3804 Dihedral : 7.488 52.572 3472 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.51 % Allowed : 11.89 % Favored : 86.60 % 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: 3.01 (0.16), residues: 2624 helix: 2.55 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.004 0.001 HIS B 92 PHE 0.018 0.001 PHE C 341 TYR 0.012 0.001 TYR A 524 ARG 0.008 0.000 ARG D 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 362 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 326 time to evaluate : 2.741 Fit side-chains REVERT: A 41 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6006 (mt-10) REVERT: A 170 ARG cc_start: 0.6663 (mtp180) cc_final: 0.5695 (ptt180) REVERT: A 222 ARG cc_start: 0.6615 (ptp-170) cc_final: 0.5795 (mtm-85) REVERT: A 253 LYS cc_start: 0.5997 (tttt) cc_final: 0.5667 (ttpp) REVERT: A 257 ASP cc_start: 0.6806 (m-30) cc_final: 0.6361 (m-30) REVERT: A 272 ARG cc_start: 0.6045 (mtt180) cc_final: 0.5161 (mtt-85) REVERT: A 337 ILE cc_start: 0.5836 (mm) cc_final: 0.5620 (mp) REVERT: A 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7435 (pm20) REVERT: A 551 ASN cc_start: 0.7584 (t0) cc_final: 0.7215 (t0) REVERT: A 636 ASP cc_start: 0.6502 (m-30) cc_final: 0.6160 (t70) REVERT: A 728 MET cc_start: 0.6280 (mmt) cc_final: 0.5927 (mmp) REVERT: A 745 GLU cc_start: 0.5345 (mt-10) cc_final: 0.5089 (mt-10) REVERT: B 41 GLU cc_start: 0.6242 (mt-10) cc_final: 0.6006 (mt-10) REVERT: B 170 ARG cc_start: 0.6664 (mtp180) cc_final: 0.5696 (ptt180) REVERT: B 222 ARG cc_start: 0.6615 (ptp-170) cc_final: 0.5796 (mtm-85) REVERT: B 253 LYS cc_start: 0.5996 (tttt) cc_final: 0.5667 (ttpp) REVERT: B 257 ASP cc_start: 0.6804 (m-30) cc_final: 0.6360 (m-30) REVERT: B 272 ARG cc_start: 0.6006 (mtt180) cc_final: 0.5118 (mtt-85) REVERT: B 337 ILE cc_start: 0.5832 (mm) cc_final: 0.5619 (mp) REVERT: B 467 GLU cc_start: 0.7777 (mp0) cc_final: 0.7420 (pm20) REVERT: B 551 ASN cc_start: 0.7583 (t0) cc_final: 0.7214 (t0) REVERT: B 636 ASP cc_start: 0.6503 (m-30) cc_final: 0.6160 (t70) REVERT: B 728 MET cc_start: 0.6281 (mmt) cc_final: 0.5930 (mmp) REVERT: B 745 GLU cc_start: 0.5346 (mt-10) cc_final: 0.5089 (mt-10) REVERT: C 41 GLU cc_start: 0.6244 (mt-10) cc_final: 0.6006 (mt-10) REVERT: C 170 ARG cc_start: 0.6659 (mtp180) cc_final: 0.5702 (ptt180) REVERT: C 222 ARG cc_start: 0.6614 (ptp-170) cc_final: 0.5795 (mtm-85) REVERT: C 253 LYS cc_start: 0.5997 (tttt) cc_final: 0.5666 (ttpp) REVERT: C 257 ASP cc_start: 0.6805 (m-30) cc_final: 0.6361 (m-30) REVERT: C 272 ARG cc_start: 0.6045 (mtt180) cc_final: 0.5162 (mtt-85) REVERT: C 337 ILE cc_start: 0.5837 (mm) cc_final: 0.5623 (mp) REVERT: C 467 GLU cc_start: 0.7774 (mp0) cc_final: 0.7420 (pm20) REVERT: C 551 ASN cc_start: 0.7584 (t0) cc_final: 0.7216 (t0) REVERT: C 636 ASP cc_start: 0.6504 (m-30) cc_final: 0.6159 (t70) REVERT: C 728 MET cc_start: 0.6283 (mmt) cc_final: 0.5929 (mmp) REVERT: C 745 GLU cc_start: 0.5346 (mt-10) cc_final: 0.5090 (mt-10) REVERT: D 41 GLU cc_start: 0.6243 (mt-10) cc_final: 0.6005 (mt-10) REVERT: D 170 ARG cc_start: 0.6659 (mtp180) cc_final: 0.5702 (ptt180) REVERT: D 222 ARG cc_start: 0.6613 (ptp-170) cc_final: 0.5794 (mtm-85) REVERT: D 253 LYS cc_start: 0.5998 (tttt) cc_final: 0.5667 (ttpp) REVERT: D 257 ASP cc_start: 0.6807 (m-30) cc_final: 0.6363 (m-30) REVERT: D 272 ARG cc_start: 0.6046 (mtt180) cc_final: 0.5162 (mtt-85) REVERT: D 337 ILE cc_start: 0.5837 (mm) cc_final: 0.5622 (mp) REVERT: D 467 GLU cc_start: 0.7775 (mp0) cc_final: 0.7433 (pm20) REVERT: D 551 ASN cc_start: 0.7584 (t0) cc_final: 0.7217 (t0) REVERT: D 636 ASP cc_start: 0.6503 (m-30) cc_final: 0.6161 (t70) REVERT: D 728 MET cc_start: 0.6281 (mmt) cc_final: 0.5929 (mmp) REVERT: D 745 GLU cc_start: 0.5342 (mt-10) cc_final: 0.5086 (mt-10) outliers start: 36 outliers final: 8 residues processed: 346 average time/residue: 1.3400 time to fit residues: 528.1929 Evaluate side-chains 326 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 318 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 739 THR 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: 0.9990 chunk 3 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS A 163 GLN A 629 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 163 GLN B 629 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS C 163 GLN C 629 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 163 GLN D 629 GLN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 22904 Z= 0.373 Angle : 0.558 7.886 31008 Z= 0.283 Chirality : 0.040 0.150 3464 Planarity : 0.004 0.041 3804 Dihedral : 8.208 57.814 3472 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.55 % Allowed : 11.52 % Favored : 86.93 % 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: 2.30 (0.16), residues: 2624 helix: 2.01 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 315 HIS 0.006 0.001 HIS A 473 PHE 0.018 0.002 PHE B 341 TYR 0.016 0.002 TYR B 524 ARG 0.009 0.001 ARG C 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 360 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 323 time to evaluate : 2.426 Fit side-chains REVERT: A 41 GLU cc_start: 0.6286 (mt-10) cc_final: 0.6017 (mt-10) REVERT: A 170 ARG cc_start: 0.6773 (mtp180) cc_final: 0.5831 (ptt180) REVERT: A 272 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5187 (mtt-85) REVERT: A 337 ILE cc_start: 0.5827 (mm) cc_final: 0.5581 (mp) REVERT: A 467 GLU cc_start: 0.7776 (mp0) cc_final: 0.7486 (pm20) REVERT: A 528 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6479 (tp) REVERT: A 551 ASN cc_start: 0.7725 (t0) cc_final: 0.7237 (t0) REVERT: A 629 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: A 636 ASP cc_start: 0.6619 (m-30) cc_final: 0.6209 (t70) REVERT: A 728 MET cc_start: 0.6495 (mmt) cc_final: 0.6130 (mmt) REVERT: A 745 GLU cc_start: 0.5306 (mt-10) cc_final: 0.5092 (mt-10) REVERT: B 41 GLU cc_start: 0.6301 (mt-10) cc_final: 0.6028 (mt-10) REVERT: B 170 ARG cc_start: 0.6775 (mtp180) cc_final: 0.5832 (ptt180) REVERT: B 272 ARG cc_start: 0.6111 (mtt180) cc_final: 0.5188 (mtt-85) REVERT: B 337 ILE cc_start: 0.5827 (mm) cc_final: 0.5581 (mp) REVERT: B 467 GLU cc_start: 0.7775 (mp0) cc_final: 0.7484 (pm20) REVERT: B 528 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6457 (tp) REVERT: B 551 ASN cc_start: 0.7717 (t0) cc_final: 0.7234 (t0) REVERT: B 636 ASP cc_start: 0.6619 (m-30) cc_final: 0.6211 (t70) REVERT: B 728 MET cc_start: 0.6496 (mmt) cc_final: 0.6131 (mmt) REVERT: B 745 GLU cc_start: 0.5307 (mt-10) cc_final: 0.5093 (mt-10) REVERT: C 41 GLU cc_start: 0.6287 (mt-10) cc_final: 0.6018 (mt-10) REVERT: C 170 ARG cc_start: 0.6776 (mtp180) cc_final: 0.5833 (ptt180) REVERT: C 272 ARG cc_start: 0.6111 (mtt180) cc_final: 0.5187 (mtt-85) REVERT: C 337 ILE cc_start: 0.5827 (mm) cc_final: 0.5582 (mp) REVERT: C 467 GLU cc_start: 0.7773 (mp0) cc_final: 0.7464 (pm20) REVERT: C 528 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6483 (tp) REVERT: C 551 ASN cc_start: 0.7732 (t0) cc_final: 0.7250 (t0) REVERT: C 636 ASP cc_start: 0.6619 (m-30) cc_final: 0.6210 (t70) REVERT: C 728 MET cc_start: 0.6497 (mmt) cc_final: 0.6131 (mmt) REVERT: C 745 GLU cc_start: 0.5306 (mt-10) cc_final: 0.5093 (mt-10) REVERT: D 41 GLU cc_start: 0.6286 (mt-10) cc_final: 0.6017 (mt-10) REVERT: D 170 ARG cc_start: 0.6775 (mtp180) cc_final: 0.5832 (ptt180) REVERT: D 272 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5187 (mtt-85) REVERT: D 337 ILE cc_start: 0.5828 (mm) cc_final: 0.5582 (mp) REVERT: D 467 GLU cc_start: 0.7775 (mp0) cc_final: 0.7485 (pm20) REVERT: D 528 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6480 (tp) REVERT: D 551 ASN cc_start: 0.7725 (t0) cc_final: 0.7237 (t0) REVERT: D 629 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6877 (mt0) REVERT: D 636 ASP cc_start: 0.6620 (m-30) cc_final: 0.6211 (t70) REVERT: D 728 MET cc_start: 0.6495 (mmt) cc_final: 0.6130 (mmt) REVERT: D 745 GLU cc_start: 0.5301 (mt-10) cc_final: 0.5088 (mt-10) outliers start: 37 outliers final: 8 residues processed: 346 average time/residue: 1.2913 time to fit residues: 509.8011 Evaluate side-chains 304 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 290 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 212 optimal weight: 0.2980 chunk 118 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS A 629 GLN A 711 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6772 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22904 Z= 0.144 Angle : 0.443 7.980 31008 Z= 0.227 Chirality : 0.035 0.148 3464 Planarity : 0.003 0.038 3804 Dihedral : 7.735 54.803 3472 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.63 % Allowed : 12.94 % Favored : 85.43 % 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: 2.30 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.003 0.000 HIS B 92 PHE 0.018 0.001 PHE C 341 TYR 0.011 0.001 TYR C 524 ARG 0.009 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 359 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 320 time to evaluate : 2.605 Fit side-chains REVERT: A 41 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5987 (mt-10) REVERT: A 170 ARG cc_start: 0.6758 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: A 272 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5161 (mtt-85) REVERT: A 337 ILE cc_start: 0.5822 (mm) cc_final: 0.5574 (mp) REVERT: A 467 GLU cc_start: 0.7785 (mp0) cc_final: 0.7461 (pm20) REVERT: A 512 ARG cc_start: 0.6768 (mtm110) cc_final: 0.6395 (mtm110) REVERT: A 528 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6397 (tp) REVERT: A 551 ASN cc_start: 0.7579 (t0) cc_final: 0.7119 (t0) REVERT: A 636 ASP cc_start: 0.6553 (m-30) cc_final: 0.6154 (t70) REVERT: A 728 MET cc_start: 0.6453 (mmt) cc_final: 0.6214 (mmt) REVERT: A 745 GLU cc_start: 0.5228 (mt-10) cc_final: 0.5014 (mt-10) REVERT: B 41 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5984 (mt-10) REVERT: B 170 ARG cc_start: 0.6758 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: B 272 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5161 (mtt-85) REVERT: B 337 ILE cc_start: 0.5823 (mm) cc_final: 0.5575 (mp) REVERT: B 467 GLU cc_start: 0.7783 (mp0) cc_final: 0.7459 (pm20) REVERT: B 512 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6458 (mtm110) REVERT: B 528 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6381 (tp) REVERT: B 551 ASN cc_start: 0.7581 (t0) cc_final: 0.7120 (t0) REVERT: B 636 ASP cc_start: 0.6556 (m-30) cc_final: 0.6156 (t70) REVERT: B 728 MET cc_start: 0.6472 (mmt) cc_final: 0.6236 (mmt) REVERT: B 745 GLU cc_start: 0.5233 (mt-10) cc_final: 0.5018 (mt-10) REVERT: C 41 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5986 (mt-10) REVERT: C 170 ARG cc_start: 0.6759 (mtp180) cc_final: 0.5716 (ptt-90) REVERT: C 272 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5161 (mtt-85) REVERT: C 337 ILE cc_start: 0.5824 (mm) cc_final: 0.5576 (mp) REVERT: C 467 GLU cc_start: 0.7782 (mp0) cc_final: 0.7460 (pm20) REVERT: C 512 ARG cc_start: 0.6829 (mtm110) cc_final: 0.6460 (mtm110) REVERT: C 528 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6363 (tp) REVERT: C 551 ASN cc_start: 0.7582 (t0) cc_final: 0.7121 (t0) REVERT: C 636 ASP cc_start: 0.6556 (m-30) cc_final: 0.6156 (t70) REVERT: C 728 MET cc_start: 0.6455 (mmt) cc_final: 0.6215 (mmt) REVERT: C 745 GLU cc_start: 0.5228 (mt-10) cc_final: 0.5015 (mt-10) REVERT: D 41 GLU cc_start: 0.6220 (mt-10) cc_final: 0.5986 (mt-10) REVERT: D 170 ARG cc_start: 0.6758 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: D 272 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5162 (mtt-85) REVERT: D 337 ILE cc_start: 0.5823 (mm) cc_final: 0.5575 (mp) REVERT: D 467 GLU cc_start: 0.7783 (mp0) cc_final: 0.7460 (pm20) REVERT: D 512 ARG cc_start: 0.6770 (mtm110) cc_final: 0.6396 (mtm110) REVERT: D 528 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6398 (tp) REVERT: D 551 ASN cc_start: 0.7580 (t0) cc_final: 0.7121 (t0) REVERT: D 636 ASP cc_start: 0.6554 (m-30) cc_final: 0.6154 (t70) REVERT: D 728 MET cc_start: 0.6472 (mmt) cc_final: 0.6237 (mmt) REVERT: D 745 GLU cc_start: 0.5253 (mt-10) cc_final: 0.5039 (mt-10) outliers start: 39 outliers final: 8 residues processed: 339 average time/residue: 1.3393 time to fit residues: 517.7275 Evaluate side-chains 307 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 295 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 0.0980 chunk 186 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 0.0980 chunk 142 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 629 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 629 GLN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22904 Z= 0.279 Angle : 0.505 10.360 31008 Z= 0.257 Chirality : 0.038 0.190 3464 Planarity : 0.004 0.037 3804 Dihedral : 7.941 55.757 3472 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.63 % Allowed : 13.65 % Favored : 84.72 % 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: 2.45 (0.16), residues: 2624 helix: 2.14 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.004 0.001 HIS D 92 PHE 0.014 0.002 PHE D 520 TYR 0.014 0.001 TYR B 524 ARG 0.009 0.000 ARG D 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 342 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 303 time to evaluate : 3.125 Fit side-chains REVERT: A 41 GLU cc_start: 0.6265 (mt-10) cc_final: 0.6016 (mt-10) REVERT: A 170 ARG cc_start: 0.6779 (mtp180) cc_final: 0.5836 (ptt180) REVERT: A 272 ARG cc_start: 0.6076 (mtt180) cc_final: 0.5159 (mtt-85) REVERT: A 337 ILE cc_start: 0.5829 (mm) cc_final: 0.5586 (mp) REVERT: A 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7500 (pm20) REVERT: A 512 ARG cc_start: 0.6784 (mtm110) cc_final: 0.6395 (mtm110) REVERT: A 528 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6466 (tp) REVERT: A 551 ASN cc_start: 0.7683 (t0) cc_final: 0.7198 (t0) REVERT: A 636 ASP cc_start: 0.6624 (m-30) cc_final: 0.6218 (t70) REVERT: B 41 GLU cc_start: 0.6267 (mt-10) cc_final: 0.6017 (mt-10) REVERT: B 170 ARG cc_start: 0.6780 (mtp180) cc_final: 0.5837 (ptt180) REVERT: B 272 ARG cc_start: 0.6077 (mtt180) cc_final: 0.5160 (mtt-85) REVERT: B 337 ILE cc_start: 0.5828 (mm) cc_final: 0.5585 (mp) REVERT: B 467 GLU cc_start: 0.7777 (mp0) cc_final: 0.7499 (pm20) REVERT: B 512 ARG cc_start: 0.6845 (mtm110) cc_final: 0.6456 (mtm110) REVERT: B 528 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6395 (tp) REVERT: B 551 ASN cc_start: 0.7674 (t0) cc_final: 0.7187 (t0) REVERT: B 636 ASP cc_start: 0.6624 (m-30) cc_final: 0.6218 (t70) REVERT: C 41 GLU cc_start: 0.6267 (mt-10) cc_final: 0.6017 (mt-10) REVERT: C 170 ARG cc_start: 0.6782 (mtp180) cc_final: 0.5838 (ptt180) REVERT: C 272 ARG cc_start: 0.6077 (mtt180) cc_final: 0.5161 (mtt-85) REVERT: C 337 ILE cc_start: 0.5804 (mm) cc_final: 0.5561 (mp) REVERT: C 467 GLU cc_start: 0.7776 (mp0) cc_final: 0.7500 (pm20) REVERT: C 512 ARG cc_start: 0.6848 (mtm110) cc_final: 0.6454 (mtm110) REVERT: C 528 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6464 (tp) REVERT: C 551 ASN cc_start: 0.7684 (t0) cc_final: 0.7200 (t0) REVERT: C 636 ASP cc_start: 0.6623 (m-30) cc_final: 0.6218 (t70) REVERT: D 41 GLU cc_start: 0.6266 (mt-10) cc_final: 0.6015 (mt-10) REVERT: D 170 ARG cc_start: 0.6782 (mtp180) cc_final: 0.5839 (ptt180) REVERT: D 272 ARG cc_start: 0.6076 (mtt180) cc_final: 0.5160 (mtt-85) REVERT: D 337 ILE cc_start: 0.5829 (mm) cc_final: 0.5587 (mp) REVERT: D 467 GLU cc_start: 0.7778 (mp0) cc_final: 0.7502 (pm20) REVERT: D 512 ARG cc_start: 0.6789 (mtm110) cc_final: 0.6399 (mtm110) REVERT: D 528 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6466 (tp) REVERT: D 551 ASN cc_start: 0.7679 (t0) cc_final: 0.7210 (t0) REVERT: D 636 ASP cc_start: 0.6624 (m-30) cc_final: 0.6218 (t70) outliers start: 39 outliers final: 12 residues processed: 324 average time/residue: 1.3153 time to fit residues: 487.7130 Evaluate side-chains 309 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 293 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 173 optimal weight: 0.0170 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN B 92 HIS B 629 GLN C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN D 92 HIS D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22904 Z= 0.164 Angle : 0.450 8.838 31008 Z= 0.229 Chirality : 0.035 0.178 3464 Planarity : 0.003 0.035 3804 Dihedral : 7.630 53.949 3472 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.55 % Allowed : 13.94 % Favored : 84.51 % 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: 2.68 (0.16), residues: 2624 helix: 2.32 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 315 HIS 0.004 0.001 HIS C 92 PHE 0.017 0.001 PHE B 520 TYR 0.012 0.001 TYR B 524 ARG 0.008 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 350 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 313 time to evaluate : 2.354 Fit side-chains REVERT: A 41 GLU cc_start: 0.6203 (mt-10) cc_final: 0.5949 (mt-10) REVERT: A 170 ARG cc_start: 0.6758 (mtp180) cc_final: 0.5718 (ptt-90) REVERT: A 272 ARG cc_start: 0.6046 (mtt180) cc_final: 0.5129 (mtt-85) REVERT: A 337 ILE cc_start: 0.5836 (mm) cc_final: 0.5611 (mp) REVERT: A 422 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.4942 (tpt) REVERT: A 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7488 (pm20) REVERT: A 528 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6400 (tp) REVERT: A 551 ASN cc_start: 0.7579 (t0) cc_final: 0.7126 (t0) REVERT: A 617 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5866 (mm) REVERT: A 636 ASP cc_start: 0.6513 (m-30) cc_final: 0.6119 (t70) REVERT: B 41 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5929 (mt-10) REVERT: B 170 ARG cc_start: 0.6759 (mtp180) cc_final: 0.5719 (ptt-90) REVERT: B 272 ARG cc_start: 0.6046 (mtt180) cc_final: 0.5129 (mtt-85) REVERT: B 337 ILE cc_start: 0.5836 (mm) cc_final: 0.5611 (mp) REVERT: B 422 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.4921 (tpt) REVERT: B 467 GLU cc_start: 0.7778 (mp0) cc_final: 0.7487 (pm20) REVERT: B 512 ARG cc_start: 0.6804 (mtm110) cc_final: 0.6413 (mtm110) REVERT: B 528 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6379 (tp) REVERT: B 551 ASN cc_start: 0.7580 (t0) cc_final: 0.7125 (t0) REVERT: B 636 ASP cc_start: 0.6522 (m-30) cc_final: 0.6122 (t70) REVERT: C 41 GLU cc_start: 0.6171 (mt-10) cc_final: 0.5919 (mt-10) REVERT: C 170 ARG cc_start: 0.6760 (mtp180) cc_final: 0.5719 (ptt-90) REVERT: C 272 ARG cc_start: 0.6048 (mtt180) cc_final: 0.5131 (mtt-85) REVERT: C 337 ILE cc_start: 0.5824 (mm) cc_final: 0.5591 (mp) REVERT: C 422 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.4920 (tpt) REVERT: C 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7488 (pm20) REVERT: C 512 ARG cc_start: 0.6831 (mtm110) cc_final: 0.6439 (mtm110) REVERT: C 528 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6381 (tp) REVERT: C 551 ASN cc_start: 0.7581 (t0) cc_final: 0.7128 (t0) REVERT: C 636 ASP cc_start: 0.6523 (m-30) cc_final: 0.6122 (t70) REVERT: D 41 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5959 (mt-10) REVERT: D 170 ARG cc_start: 0.6760 (mtp180) cc_final: 0.5719 (ptt-90) REVERT: D 272 ARG cc_start: 0.6050 (mtt180) cc_final: 0.5136 (mtt-85) REVERT: D 337 ILE cc_start: 0.5835 (mm) cc_final: 0.5610 (mp) REVERT: D 422 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.4933 (tpt) REVERT: D 467 GLU cc_start: 0.7778 (mp0) cc_final: 0.7489 (pm20) REVERT: D 528 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6396 (tp) REVERT: D 551 ASN cc_start: 0.7579 (t0) cc_final: 0.7127 (t0) REVERT: D 636 ASP cc_start: 0.6514 (m-30) cc_final: 0.6120 (t70) outliers start: 37 outliers final: 14 residues processed: 328 average time/residue: 1.2384 time to fit residues: 468.0552 Evaluate side-chains 317 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 214 optimal weight: 0.5980 chunk 224 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 443 ASN B 629 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** C 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 629 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22904 Z= 0.310 Angle : 0.523 11.839 31008 Z= 0.266 Chirality : 0.039 0.267 3464 Planarity : 0.004 0.033 3804 Dihedral : 7.926 54.601 3472 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.42 % Allowed : 14.03 % Favored : 84.55 % 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: 2.38 (0.16), residues: 2624 helix: 2.08 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : 0.13 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 315 HIS 0.005 0.001 HIS C 92 PHE 0.021 0.002 PHE B 520 TYR 0.014 0.001 TYR C 524 ARG 0.008 0.000 ARG C 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 335 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 301 time to evaluate : 2.698 Fit side-chains REVERT: A 38 ASN cc_start: 0.6224 (t0) cc_final: 0.5848 (t0) REVERT: A 41 GLU cc_start: 0.6252 (mt-10) cc_final: 0.5997 (mt-10) REVERT: A 170 ARG cc_start: 0.6809 (mtp180) cc_final: 0.5874 (ptt180) REVERT: A 272 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5171 (mtt-85) REVERT: A 337 ILE cc_start: 0.5840 (mm) cc_final: 0.5600 (mp) REVERT: A 422 MET cc_start: 0.5576 (OUTLIER) cc_final: 0.4975 (tpt) REVERT: A 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7512 (pm20) REVERT: A 528 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6467 (tp) REVERT: A 551 ASN cc_start: 0.7605 (t0) cc_final: 0.7144 (t0) REVERT: A 629 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6831 (mm-40) REVERT: A 636 ASP cc_start: 0.6601 (m-30) cc_final: 0.6192 (t70) REVERT: B 38 ASN cc_start: 0.6224 (t0) cc_final: 0.5846 (t0) REVERT: B 41 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6021 (mt-10) REVERT: B 170 ARG cc_start: 0.6810 (mtp180) cc_final: 0.5875 (ptt180) REVERT: B 272 ARG cc_start: 0.6086 (mtt180) cc_final: 0.5171 (mtt-85) REVERT: B 337 ILE cc_start: 0.5839 (mm) cc_final: 0.5600 (mp) REVERT: B 422 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4978 (tpt) REVERT: B 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7509 (pm20) REVERT: B 512 ARG cc_start: 0.6834 (mtm110) cc_final: 0.6432 (mtm110) REVERT: B 528 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6410 (tp) REVERT: B 551 ASN cc_start: 0.7607 (t0) cc_final: 0.7146 (t0) REVERT: B 636 ASP cc_start: 0.6629 (m-30) cc_final: 0.6213 (t70) REVERT: C 38 ASN cc_start: 0.6223 (t0) cc_final: 0.5847 (t0) REVERT: C 41 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6018 (mt-10) REVERT: C 170 ARG cc_start: 0.6811 (mtp180) cc_final: 0.5876 (ptt180) REVERT: C 272 ARG cc_start: 0.6086 (mtt180) cc_final: 0.5172 (mtt-85) REVERT: C 337 ILE cc_start: 0.5838 (mm) cc_final: 0.5601 (mp) REVERT: C 422 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.4978 (tpt) REVERT: C 467 GLU cc_start: 0.7779 (mp0) cc_final: 0.7484 (pm20) REVERT: C 512 ARG cc_start: 0.6832 (mtm110) cc_final: 0.6425 (mtm110) REVERT: C 528 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6422 (tp) REVERT: C 551 ASN cc_start: 0.7608 (t0) cc_final: 0.7146 (t0) REVERT: C 636 ASP cc_start: 0.6629 (m-30) cc_final: 0.6212 (t70) REVERT: D 38 ASN cc_start: 0.6226 (t0) cc_final: 0.5849 (t0) REVERT: D 41 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5998 (mt-10) REVERT: D 170 ARG cc_start: 0.6811 (mtp180) cc_final: 0.5876 (ptt180) REVERT: D 272 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5171 (mtt-85) REVERT: D 337 ILE cc_start: 0.5840 (mm) cc_final: 0.5601 (mp) REVERT: D 422 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.4923 (tpt) REVERT: D 467 GLU cc_start: 0.7780 (mp0) cc_final: 0.7513 (pm20) REVERT: D 528 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6471 (tp) REVERT: D 551 ASN cc_start: 0.7606 (t0) cc_final: 0.7145 (t0) REVERT: D 636 ASP cc_start: 0.6601 (m-30) cc_final: 0.6194 (t70) outliers start: 34 outliers final: 10 residues processed: 319 average time/residue: 1.2598 time to fit residues: 460.3955 Evaluate side-chains 317 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 298 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 652 ASP 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: 1.9990 chunk 118 optimal weight: 0.9990 chunk 174 optimal weight: 0.2980 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 711 GLN B 92 HIS B 629 GLN B 711 GLN C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6760 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22904 Z= 0.150 Angle : 0.451 10.285 31008 Z= 0.229 Chirality : 0.036 0.216 3464 Planarity : 0.003 0.035 3804 Dihedral : 7.583 53.977 3472 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.96 % Allowed : 14.24 % Favored : 84.80 % 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: 2.67 (0.16), residues: 2624 helix: 2.31 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.14 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 315 HIS 0.003 0.000 HIS A 92 PHE 0.016 0.001 PHE D 341 TYR 0.010 0.001 TYR D 524 ARG 0.008 0.000 ARG D 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 338 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 315 time to evaluate : 2.765 Fit side-chains REVERT: A 38 ASN cc_start: 0.6304 (t0) cc_final: 0.5996 (t0) REVERT: A 41 GLU cc_start: 0.6125 (mt-10) cc_final: 0.5895 (mt-10) REVERT: A 170 ARG cc_start: 0.6739 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: A 272 ARG cc_start: 0.5976 (mtt180) cc_final: 0.5076 (mtt-85) REVERT: A 337 ILE cc_start: 0.5823 (mm) cc_final: 0.5585 (mp) REVERT: A 422 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.4899 (tpt) REVERT: A 467 GLU cc_start: 0.7802 (mp0) cc_final: 0.7499 (pm20) REVERT: A 528 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6365 (tp) REVERT: A 551 ASN cc_start: 0.7560 (t0) cc_final: 0.7121 (t0) REVERT: A 617 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5847 (mm) REVERT: A 629 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6921 (mm-40) REVERT: A 636 ASP cc_start: 0.6489 (m-30) cc_final: 0.6111 (t70) REVERT: B 38 ASN cc_start: 0.6306 (t0) cc_final: 0.5995 (t0) REVERT: B 41 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5909 (mt-10) REVERT: B 170 ARG cc_start: 0.6741 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: B 272 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5077 (mtt-85) REVERT: B 337 ILE cc_start: 0.5823 (mm) cc_final: 0.5586 (mp) REVERT: B 422 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.4902 (tpt) REVERT: B 467 GLU cc_start: 0.7801 (mp0) cc_final: 0.7497 (pm20) REVERT: B 512 ARG cc_start: 0.6820 (mtm110) cc_final: 0.6434 (mtm110) REVERT: B 528 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6404 (tp) REVERT: B 551 ASN cc_start: 0.7562 (t0) cc_final: 0.7123 (t0) REVERT: B 617 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5860 (mm) REVERT: B 629 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: B 636 ASP cc_start: 0.6514 (m-30) cc_final: 0.6117 (t70) REVERT: C 38 ASN cc_start: 0.6296 (t0) cc_final: 0.6008 (t0) REVERT: C 41 GLU cc_start: 0.6152 (mt-10) cc_final: 0.5912 (mt-10) REVERT: C 170 ARG cc_start: 0.6741 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: C 272 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5077 (mtt-85) REVERT: C 337 ILE cc_start: 0.5822 (mm) cc_final: 0.5581 (mp) REVERT: C 422 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4901 (tpt) REVERT: C 467 GLU cc_start: 0.7802 (mp0) cc_final: 0.7478 (pm20) REVERT: C 512 ARG cc_start: 0.6822 (mtm110) cc_final: 0.6430 (mtm110) REVERT: C 528 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6392 (tp) REVERT: C 551 ASN cc_start: 0.7563 (t0) cc_final: 0.7124 (t0) REVERT: C 617 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5872 (mm) REVERT: C 636 ASP cc_start: 0.6513 (m-30) cc_final: 0.6117 (t70) REVERT: D 38 ASN cc_start: 0.6298 (t0) cc_final: 0.6008 (t0) REVERT: D 41 GLU cc_start: 0.6126 (mt-10) cc_final: 0.5895 (mt-10) REVERT: D 170 ARG cc_start: 0.6741 (mtp180) cc_final: 0.5715 (ptt-90) REVERT: D 272 ARG cc_start: 0.5976 (mtt180) cc_final: 0.5077 (mtt-85) REVERT: D 337 ILE cc_start: 0.5822 (mm) cc_final: 0.5585 (mp) REVERT: D 422 MET cc_start: 0.5489 (OUTLIER) cc_final: 0.4886 (tpt) REVERT: D 467 GLU cc_start: 0.7802 (mp0) cc_final: 0.7499 (pm20) REVERT: D 528 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6365 (tp) REVERT: D 551 ASN cc_start: 0.7560 (t0) cc_final: 0.7122 (t0) REVERT: D 617 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5865 (mm) REVERT: D 636 ASP cc_start: 0.6492 (m-30) cc_final: 0.6113 (t70) outliers start: 23 outliers final: 5 residues processed: 325 average time/residue: 1.2667 time to fit residues: 471.5524 Evaluate side-chains 315 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 296 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain A residue 652 ASP Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 652 ASP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 184 optimal weight: 2.9990 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 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 711 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 629 GLN B 711 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 711 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 629 GLN D 711 GLN ** D 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.168712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130795 restraints weight = 20185.420| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.62 r_work: 0.3240 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22904 Z= 0.258 Angle : 0.500 10.988 31008 Z= 0.257 Chirality : 0.037 0.148 3464 Planarity : 0.004 0.038 3804 Dihedral : 7.770 53.812 3472 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.88 % Allowed : 14.57 % Favored : 84.55 % 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: 2.49 (0.16), residues: 2624 helix: 2.17 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.11 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 315 HIS 0.005 0.001 HIS D 92 PHE 0.019 0.002 PHE C 341 TYR 0.012 0.001 TYR D 524 ARG 0.009 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8611.39 seconds wall clock time: 153 minutes 30.50 seconds (9210.50 seconds total)