Starting phenix.real_space_refine on Sun Feb 18 17:40:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x6c_33021/02_2024/7x6c_33021.pdb" } resolution = 3.15 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= 0.144 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: 7 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 C 14840 2.51 5 N 3640 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 715": "OE1" <-> "OE2" Residue "C GLU 736": "OE1" <-> "OE2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 254": "OD1" <-> "OD2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B GLU 736": "OE1" <-> "OE2" Residue "B GLU 740": "OE1" <-> "OE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D GLU 736": "OE1" <-> "OE2" Residue "D GLU 740": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22632 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "A" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "B" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "D" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5501 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 25, 'TRANS': 649} Chain breaks: 3 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' CA': 1, ' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS C 176 62.296 98.972 74.070 1.00 72.21 S ATOM 1162 SG CYS C 178 64.600 101.780 75.305 1.00 73.13 S ATOM 1184 SG CYS C 181 65.020 98.311 76.766 1.00 63.41 S ATOM 6649 SG CYS A 176 50.627 13.965 74.119 1.00 72.01 S ATOM 6663 SG CYS A 178 48.324 11.158 75.358 1.00 72.83 S ATOM 6685 SG CYS A 181 47.902 14.627 76.815 1.00 63.43 S ATOM 12150 SG CYS B 176 99.061 50.536 74.100 1.00 71.76 S ATOM 12164 SG CYS B 178 101.869 48.233 75.337 1.00 72.76 S ATOM 12186 SG CYS B 181 98.400 47.812 76.796 1.00 61.99 S ATOM 17651 SG CYS D 176 13.838 62.396 74.082 1.00 71.38 S ATOM 17665 SG CYS D 178 11.029 64.699 75.316 1.00 72.17 S ATOM 17687 SG CYS D 181 14.497 65.123 76.776 1.00 62.05 S Time building chain proxies: 12.44, per 1000 atoms: 0.55 Number of scatterers: 22632 At special positions: 0 Unit cell: (114.03, 114.03, 137.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 4020 8.00 N 3640 7.00 C 14840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 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 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: 9.21 Conformation dependent library (CDL) restraints added in 4.2 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 181 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - 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 181 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb=" ZN D 805 " pdb="ZN ZN D 805 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 176 " Number of angles added : 12 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 74.1% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.581A pdb=" N PHE C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.614A pdb=" N MET C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.857A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 257 removed outlier: 3.789A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) 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 345 through 351 Processing helix chain 'C' and resid 362 through 384 Processing helix chain 'C' and resid 401 through 424 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP C 469 " --> pdb=" O ARG C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 3.936A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.102A 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 549 through 553 removed outlier: 3.510A pdb=" N ASN C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 588 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 632 Processing helix chain 'C' and resid 635 through 649 removed outlier: 3.728A pdb=" N TRP C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 649 " --> pdb=" O LYS C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 732 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'A' and resid 30 through 43 removed outlier: 3.581A pdb=" N PHE A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.615A pdb=" N MET A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.907A pdb=" N SER A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.856A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 257 removed outlier: 3.789A pdb=" N TYR A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) 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 345 through 351 Processing helix chain 'A' and resid 362 through 384 Processing helix chain 'A' and resid 401 through 424 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP A 469 " --> pdb=" O ARG A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 499 removed outlier: 4.129A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 3.935A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.101A 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 549 through 553 removed outlier: 3.511A pdb=" N ASN A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.823A pdb=" N VAL A 587 " --> pdb=" O ASN A 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 632 Processing helix chain 'A' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP A 639 " --> pdb=" O ALA A 635 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 649 " --> pdb=" O LYS A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 732 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.582A pdb=" N PHE B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.615A pdb=" N MET B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 108 through 117 removed outlier: 3.593A pdb=" N VAL B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.855A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 257 removed outlier: 3.788A pdb=" N TYR B 241 " --> pdb=" O PHE B 237 " (cutoff:3.500A) 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 345 through 351 Processing helix chain 'B' and resid 362 through 384 Processing helix chain 'B' and resid 401 through 424 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.562A pdb=" N TRP B 469 " --> pdb=" O ARG B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 3.936A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.101A 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 549 through 553 removed outlier: 3.511A pdb=" N ASN B 552 " --> pdb=" O GLU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL B 587 " --> pdb=" O ASN B 584 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 588 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP B 639 " --> pdb=" O ALA B 635 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 649 " --> pdb=" O LYS B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 732 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.582A pdb=" N PHE D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.614A pdb=" N MET D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 108 through 117 removed outlier: 3.594A pdb=" N VAL D 112 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.906A pdb=" N SER D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.855A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 257 removed outlier: 3.788A pdb=" N TYR D 241 " --> pdb=" O PHE D 237 " (cutoff:3.500A) 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 345 through 351 Processing helix chain 'D' and resid 362 through 384 Processing helix chain 'D' and resid 401 through 424 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.563A pdb=" N TRP D 469 " --> pdb=" O ARG D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 499 removed outlier: 4.130A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 3.935A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 519 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.102A 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 549 through 553 removed outlier: 3.511A pdb=" N ASN D 552 " --> pdb=" O GLU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.824A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 632 Processing helix chain 'D' and resid 635 through 649 removed outlier: 3.729A pdb=" N TRP D 639 " --> pdb=" O ALA D 635 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 649 " --> pdb=" O LYS D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 732 Processing helix chain 'D' and resid 734 through 758 Processing sheet with id=AA1, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 1384 hydrogen bonds defined for protein. 4068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3568 1.32 - 1.44: 6208 1.44 - 1.56: 13168 1.56 - 1.69: 20 1.69 - 1.81: 188 Bond restraints: 23152 Sorted by residual: bond pdb=" O12 POV C 802 " pdb=" P POV C 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV D 803 " pdb=" P POV D 803 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" O12 POV B 803 " pdb=" P POV B 803 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" O12 POV A 802 " pdb=" P POV A 802 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.39e+00 bond pdb=" C1 POV B 803 " pdb=" O11 POV B 803 " ideal model delta sigma weight residual 1.410 1.459 -0.049 2.00e-02 2.50e+03 5.95e+00 ... (remaining 23147 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.20: 556 106.20 - 113.19: 12438 113.19 - 120.18: 8500 120.18 - 127.17: 9539 127.17 - 134.16: 275 Bond angle restraints: 31308 Sorted by residual: angle pdb=" C ILE D 729 " pdb=" N ARG D 730 " pdb=" CA ARG D 730 " ideal model delta sigma weight residual 122.26 112.04 10.22 1.73e+00 3.34e-01 3.49e+01 angle pdb=" C ILE A 729 " pdb=" N ARG A 730 " pdb=" CA ARG A 730 " ideal model delta sigma weight residual 122.26 112.08 10.18 1.73e+00 3.34e-01 3.46e+01 angle pdb=" C ILE B 729 " pdb=" N ARG B 730 " pdb=" CA ARG B 730 " ideal model delta sigma weight residual 122.26 112.08 10.18 1.73e+00 3.34e-01 3.46e+01 angle pdb=" C ILE C 729 " pdb=" N ARG C 730 " pdb=" CA ARG C 730 " ideal model delta sigma weight residual 122.26 112.10 10.16 1.73e+00 3.34e-01 3.45e+01 angle pdb=" CA GLU B 81 " pdb=" CB GLU B 81 " pdb=" CG GLU B 81 " ideal model delta sigma weight residual 114.10 125.53 -11.43 2.00e+00 2.50e-01 3.26e+01 ... (remaining 31303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 13744 35.59 - 71.19: 341 71.19 - 106.78: 23 106.78 - 142.38: 20 142.38 - 177.97: 4 Dihedral angle restraints: 14132 sinusoidal: 6136 harmonic: 7996 Sorted by residual: dihedral pdb=" C26 YZY D 801 " pdb=" C27 YZY D 801 " pdb=" C28 YZY D 801 " pdb=" C29 YZY D 801 " ideal model delta sinusoidal sigma weight residual 119.11 -58.86 177.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -58.84 177.95 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY B 801 " pdb=" C27 YZY B 801 " pdb=" C28 YZY B 801 " pdb=" C29 YZY B 801 " ideal model delta sinusoidal sigma weight residual 119.11 -58.81 177.92 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 14129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2586 0.044 - 0.088: 749 0.088 - 0.131: 137 0.131 - 0.175: 12 0.175 - 0.219: 12 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CB VAL A 96 " pdb=" CA VAL A 96 " pdb=" CG1 VAL A 96 " pdb=" CG2 VAL A 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL D 96 " pdb=" CA VAL D 96 " pdb=" CG1 VAL D 96 " pdb=" CG2 VAL D 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB VAL C 96 " pdb=" CA VAL C 96 " pdb=" CG1 VAL C 96 " pdb=" CG2 VAL C 96 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3493 not shown) Planarity restraints: 3860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY A 806 " 0.058 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C28 YZY A 806 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY A 806 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY A 806 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY D 801 " 0.058 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C28 YZY D 801 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY D 801 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY D 801 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 801 " 0.058 2.00e-02 2.50e+03 5.80e-02 3.37e+01 pdb=" C28 YZY B 801 " -0.059 2.00e-02 2.50e+03 pdb=" C29 YZY B 801 " -0.057 2.00e-02 2.50e+03 pdb=" C30 YZY B 801 " 0.058 2.00e-02 2.50e+03 ... (remaining 3857 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4577 2.78 - 3.31: 20921 3.31 - 3.84: 36619 3.84 - 4.37: 42157 4.37 - 4.90: 76147 Nonbonded interactions: 180421 Sorted by model distance: nonbonded pdb=" O HIS D 735 " pdb=" OG1 THR D 739 " model vdw 2.249 2.440 nonbonded pdb=" O HIS B 735 " pdb=" OG1 THR B 739 " model vdw 2.249 2.440 nonbonded pdb=" O HIS C 735 " pdb=" OG1 THR C 739 " model vdw 2.250 2.440 nonbonded pdb=" O HIS A 735 " pdb=" OG1 THR A 739 " model vdw 2.250 2.440 nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.258 2.440 ... (remaining 180416 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 758) selection = (chain 'B' and resid 17 through 758) selection = (chain 'C' and resid 17 through 758) selection = (chain 'D' and resid 17 through 758) } 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: 4.380 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: 0.020 Extract box with map and model: 14.650 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 64.100 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.004 0.066 23152 Z= 0.282 Angle : 0.735 11.426 31308 Z= 0.383 Chirality : 0.042 0.219 3496 Planarity : 0.006 0.067 3860 Dihedral : 16.820 177.972 8920 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.66 % Allowed : 1.00 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2668 helix: 0.34 (0.11), residues: 1884 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 410 HIS 0.003 0.000 HIS C 192 PHE 0.030 0.002 PHE D 743 TYR 0.025 0.001 TYR B 541 ARG 0.008 0.001 ARG B 730 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 312 time to evaluate : 2.600 Fit side-chains REVERT: C 551 ASN cc_start: 0.7513 (t0) cc_final: 0.7167 (t0) REVERT: A 741 GLU cc_start: 0.7397 (tp30) cc_final: 0.6985 (tp30) REVERT: B 516 ASP cc_start: 0.6720 (m-30) cc_final: 0.6291 (m-30) REVERT: D 516 ASP cc_start: 0.6773 (m-30) cc_final: 0.6333 (m-30) REVERT: D 631 ILE cc_start: 0.8157 (tp) cc_final: 0.7937 (tp) outliers start: 16 outliers final: 2 residues processed: 318 average time/residue: 0.3138 time to fit residues: 160.2062 Evaluate side-chains 265 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain A residue 648 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN B 163 GLN ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 742 ASN D 163 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 23152 Z= 0.460 Angle : 0.635 5.679 31308 Z= 0.331 Chirality : 0.042 0.142 3496 Planarity : 0.005 0.045 3860 Dihedral : 13.149 149.015 3606 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.00 % Allowed : 4.81 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2668 helix: 0.98 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -1.01 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 315 HIS 0.007 0.001 HIS D 172 PHE 0.018 0.003 PHE A 580 TYR 0.020 0.002 TYR B 524 ARG 0.003 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 2.811 Fit side-chains REVERT: B 106 LYS cc_start: 0.8272 (tptt) cc_final: 0.8067 (tptt) REVERT: D 172 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6245 (t-90) outliers start: 24 outliers final: 15 residues processed: 281 average time/residue: 0.3234 time to fit residues: 144.6914 Evaluate side-chains 265 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.0570 chunk 75 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN C 742 ASN A 163 GLN A 625 ASN A 629 GLN B 163 GLN B 625 ASN B 629 GLN D 163 GLN D 625 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23152 Z= 0.182 Angle : 0.456 5.846 31308 Z= 0.242 Chirality : 0.036 0.140 3496 Planarity : 0.004 0.039 3860 Dihedral : 11.389 145.071 3600 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.75 % Allowed : 7.75 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.16), residues: 2668 helix: 1.66 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.94 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 315 HIS 0.008 0.000 HIS D 172 PHE 0.021 0.001 PHE C 427 TYR 0.016 0.001 TYR A 524 ARG 0.004 0.000 ARG C 730 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 273 time to evaluate : 2.399 Fit side-chains REVERT: C 355 ASN cc_start: 0.7463 (t0) cc_final: 0.7231 (t0) REVERT: C 631 ILE cc_start: 0.8269 (tp) cc_final: 0.7966 (tp) REVERT: A 355 ASN cc_start: 0.7465 (t0) cc_final: 0.7244 (t0) REVERT: A 631 ILE cc_start: 0.8288 (tp) cc_final: 0.8000 (tp) REVERT: B 516 ASP cc_start: 0.6712 (m-30) cc_final: 0.6426 (m-30) REVERT: B 657 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7846 (mm) REVERT: D 172 HIS cc_start: 0.7162 (OUTLIER) cc_final: 0.6152 (t-90) REVERT: D 631 ILE cc_start: 0.8279 (tp) cc_final: 0.8023 (tp) outliers start: 18 outliers final: 10 residues processed: 280 average time/residue: 0.3386 time to fit residues: 153.7135 Evaluate side-chains 269 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 257 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 625 ASN Chi-restraints excluded: chain D residue 634 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 244 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN C 742 ASN A 163 GLN A 629 GLN A 742 ASN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23152 Z= 0.206 Angle : 0.457 5.908 31308 Z= 0.241 Chirality : 0.036 0.130 3496 Planarity : 0.004 0.039 3860 Dihedral : 10.850 144.143 3600 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.83 % Allowed : 9.33 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2668 helix: 1.87 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.85 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 315 HIS 0.007 0.001 HIS D 172 PHE 0.023 0.001 PHE B 427 TYR 0.016 0.001 TYR A 524 ARG 0.005 0.000 ARG C 730 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 2.464 Fit side-chains REVERT: C 355 ASN cc_start: 0.7693 (t0) cc_final: 0.7490 (t0) REVERT: C 631 ILE cc_start: 0.8249 (tp) cc_final: 0.7940 (tp) REVERT: C 730 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7232 (ttt-90) REVERT: A 631 ILE cc_start: 0.8292 (tp) cc_final: 0.7995 (tp) REVERT: A 730 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7244 (ttt-90) REVERT: B 657 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7816 (mm) REVERT: B 730 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7272 (ttt-90) REVERT: D 172 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.6147 (t-90) REVERT: D 631 ILE cc_start: 0.8311 (tp) cc_final: 0.8013 (tp) REVERT: D 730 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7223 (ttt-90) outliers start: 20 outliers final: 12 residues processed: 278 average time/residue: 0.3109 time to fit residues: 139.2554 Evaluate side-chains 273 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN A 163 GLN A 629 GLN A 742 ASN B 163 GLN B 629 GLN B 742 ASN D 163 GLN D 629 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23152 Z= 0.346 Angle : 0.535 6.019 31308 Z= 0.279 Chirality : 0.039 0.133 3496 Planarity : 0.004 0.044 3860 Dihedral : 11.032 146.799 3600 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.91 % Allowed : 11.73 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2668 helix: 1.68 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.88 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 315 HIS 0.007 0.001 HIS D 172 PHE 0.024 0.002 PHE C 427 TYR 0.017 0.001 TYR A 524 ARG 0.004 0.000 ARG B 730 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 279 time to evaluate : 2.581 Fit side-chains REVERT: C 343 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6174 (tmm) REVERT: C 434 TRP cc_start: 0.6967 (m100) cc_final: 0.6410 (m100) REVERT: C 631 ILE cc_start: 0.8289 (tp) cc_final: 0.7987 (tp) REVERT: A 343 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.6146 (tmm) REVERT: A 434 TRP cc_start: 0.6975 (m100) cc_final: 0.6207 (m100) REVERT: A 631 ILE cc_start: 0.8324 (tp) cc_final: 0.8006 (tp) REVERT: A 730 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7226 (ttt-90) REVERT: B 427 PHE cc_start: 0.8236 (t80) cc_final: 0.8026 (t80) REVERT: B 516 ASP cc_start: 0.6805 (m-30) cc_final: 0.6514 (m-30) REVERT: B 619 MET cc_start: 0.6770 (ttt) cc_final: 0.6483 (ttt) REVERT: B 657 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7981 (mm) REVERT: B 715 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6815 (mp0) REVERT: B 730 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7217 (ttt-90) REVERT: D 172 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6144 (t-90) REVERT: D 427 PHE cc_start: 0.8227 (t80) cc_final: 0.8005 (t80) REVERT: D 631 ILE cc_start: 0.8284 (tp) cc_final: 0.8006 (tp) REVERT: D 715 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6809 (mp0) outliers start: 22 outliers final: 14 residues processed: 287 average time/residue: 0.3331 time to fit residues: 153.8401 Evaluate side-chains 284 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 266 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 259 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN B 163 GLN B 629 GLN D 163 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23152 Z= 0.214 Angle : 0.460 5.947 31308 Z= 0.245 Chirality : 0.036 0.130 3496 Planarity : 0.004 0.041 3860 Dihedral : 10.738 146.401 3600 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.87 % Allowed : 11.98 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.17), residues: 2668 helix: 1.87 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 315 HIS 0.007 0.001 HIS D 172 PHE 0.026 0.001 PHE A 427 TYR 0.016 0.001 TYR A 524 ARG 0.003 0.000 ARG A 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 2.393 Fit side-chains REVERT: C 631 ILE cc_start: 0.8259 (tp) cc_final: 0.7990 (tp) REVERT: A 631 ILE cc_start: 0.8276 (tp) cc_final: 0.8003 (tp) REVERT: B 657 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7981 (mm) REVERT: D 172 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6118 (t-90) REVERT: D 434 TRP cc_start: 0.6947 (m100) cc_final: 0.6377 (m100) REVERT: D 631 ILE cc_start: 0.8300 (tp) cc_final: 0.8009 (tp) REVERT: D 657 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7954 (mm) outliers start: 21 outliers final: 15 residues processed: 273 average time/residue: 0.3011 time to fit residues: 133.5327 Evaluate side-chains 267 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 470 GLU Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 0.0570 chunk 189 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 161 optimal weight: 0.0870 chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN A 742 ASN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23152 Z= 0.131 Angle : 0.408 5.917 31308 Z= 0.220 Chirality : 0.035 0.129 3496 Planarity : 0.004 0.037 3860 Dihedral : 10.219 144.218 3600 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.62 % Allowed : 12.56 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.17), residues: 2668 helix: 2.20 (0.12), residues: 1916 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 315 HIS 0.006 0.000 HIS D 172 PHE 0.032 0.001 PHE D 427 TYR 0.015 0.001 TYR A 524 ARG 0.004 0.000 ARG D 730 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 2.711 Fit side-chains REVERT: C 631 ILE cc_start: 0.8215 (tp) cc_final: 0.7963 (tp) REVERT: A 631 ILE cc_start: 0.8273 (tp) cc_final: 0.7985 (tp) REVERT: B 631 ILE cc_start: 0.8289 (tp) cc_final: 0.8052 (tp) REVERT: B 657 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7856 (mm) REVERT: D 172 HIS cc_start: 0.7021 (OUTLIER) cc_final: 0.6031 (t-90) REVERT: D 631 ILE cc_start: 0.8287 (tp) cc_final: 0.8032 (tp) REVERT: D 657 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7873 (mm) outliers start: 15 outliers final: 7 residues processed: 282 average time/residue: 0.3028 time to fit residues: 140.0007 Evaluate side-chains 266 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 154 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 234 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23152 Z= 0.184 Angle : 0.444 5.902 31308 Z= 0.238 Chirality : 0.036 0.138 3496 Planarity : 0.004 0.039 3860 Dihedral : 10.240 144.279 3600 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.70 % Allowed : 13.27 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.17), residues: 2668 helix: 2.14 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.80 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.006 0.000 HIS D 172 PHE 0.016 0.001 PHE A 427 TYR 0.015 0.001 TYR A 524 ARG 0.003 0.000 ARG D 730 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 270 time to evaluate : 2.469 Fit side-chains REVERT: C 427 PHE cc_start: 0.8046 (t80) cc_final: 0.7836 (t80) REVERT: C 631 ILE cc_start: 0.8209 (tp) cc_final: 0.7953 (tp) REVERT: C 715 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6842 (mp0) REVERT: A 631 ILE cc_start: 0.8219 (tp) cc_final: 0.7939 (tp) REVERT: A 715 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6836 (mp0) REVERT: B 631 ILE cc_start: 0.8316 (tp) cc_final: 0.8089 (tp) REVERT: B 657 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7894 (mm) REVERT: D 172 HIS cc_start: 0.7022 (OUTLIER) cc_final: 0.6043 (t-90) REVERT: D 631 ILE cc_start: 0.8279 (tp) cc_final: 0.8010 (tp) REVERT: D 657 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7903 (mm) REVERT: D 715 GLU cc_start: 0.7219 (mp0) cc_final: 0.6944 (mp0) outliers start: 17 outliers final: 10 residues processed: 276 average time/residue: 0.2993 time to fit residues: 135.6190 Evaluate side-chains 275 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 262 time to evaluate : 2.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23152 Z= 0.301 Angle : 0.514 6.030 31308 Z= 0.272 Chirality : 0.038 0.145 3496 Planarity : 0.004 0.042 3860 Dihedral : 10.631 147.350 3600 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.79 % Allowed : 13.56 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2668 helix: 1.87 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.86 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 315 HIS 0.006 0.001 HIS D 172 PHE 0.026 0.002 PHE B 427 TYR 0.016 0.001 TYR B 524 ARG 0.003 0.000 ARG D 730 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 264 time to evaluate : 2.468 Fit side-chains REVERT: C 427 PHE cc_start: 0.8038 (t80) cc_final: 0.7756 (t80) REVERT: C 631 ILE cc_start: 0.8234 (tp) cc_final: 0.7976 (tp) REVERT: C 715 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6804 (mp0) REVERT: A 631 ILE cc_start: 0.8284 (tp) cc_final: 0.7992 (tp) REVERT: A 715 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6799 (mp0) REVERT: B 657 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8041 (mm) REVERT: B 715 GLU cc_start: 0.7308 (mp0) cc_final: 0.7105 (mp0) REVERT: D 172 HIS cc_start: 0.7065 (OUTLIER) cc_final: 0.6079 (t-90) REVERT: D 631 ILE cc_start: 0.8260 (tp) cc_final: 0.7991 (tp) REVERT: D 657 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8044 (mm) REVERT: D 715 GLU cc_start: 0.7292 (mp0) cc_final: 0.6915 (mp0) outliers start: 19 outliers final: 12 residues processed: 272 average time/residue: 0.3069 time to fit residues: 136.6448 Evaluate side-chains 272 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 266 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23152 Z= 0.206 Angle : 0.462 6.018 31308 Z= 0.248 Chirality : 0.036 0.130 3496 Planarity : 0.004 0.041 3860 Dihedral : 10.451 146.704 3600 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.62 % Allowed : 13.72 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.17), residues: 2668 helix: 1.98 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 315 HIS 0.006 0.001 HIS D 172 PHE 0.023 0.001 PHE A 427 TYR 0.015 0.001 TYR A 524 ARG 0.003 0.000 ARG D 730 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 2.864 Fit side-chains REVERT: C 431 ILE cc_start: 0.8642 (pt) cc_final: 0.8377 (mt) REVERT: C 631 ILE cc_start: 0.8228 (tp) cc_final: 0.7974 (tp) REVERT: C 715 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6869 (mp0) REVERT: A 431 ILE cc_start: 0.8655 (pt) cc_final: 0.8385 (mt) REVERT: A 631 ILE cc_start: 0.8237 (tp) cc_final: 0.7958 (tp) REVERT: A 715 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6867 (mp0) REVERT: B 631 ILE cc_start: 0.8320 (tp) cc_final: 0.8098 (tp) REVERT: B 657 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 715 GLU cc_start: 0.7299 (mp0) cc_final: 0.7032 (mp0) REVERT: D 172 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6038 (t-90) REVERT: D 631 ILE cc_start: 0.8243 (tp) cc_final: 0.7981 (tp) REVERT: D 657 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8007 (mm) REVERT: D 715 GLU cc_start: 0.7261 (mp0) cc_final: 0.6892 (mp0) outliers start: 15 outliers final: 11 residues processed: 266 average time/residue: 0.3051 time to fit residues: 132.3839 Evaluate side-chains 268 residues out of total 2412 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 254 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 HIS Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 634 HIS Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 634 HIS Chi-restraints excluded: chain B residue 634 HIS Chi-restraints excluded: chain B residue 652 ASP Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 657 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 186 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 629 GLN A 163 GLN A 629 GLN B 163 GLN B 629 GLN D 163 GLN D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.193027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147534 restraints weight = 21659.509| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.81 r_work: 0.3281 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23152 Z= 0.197 Angle : 0.455 6.763 31308 Z= 0.244 Chirality : 0.036 0.143 3496 Planarity : 0.004 0.040 3860 Dihedral : 10.335 146.025 3600 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.50 % Allowed : 13.85 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.17), residues: 2668 helix: 2.03 (0.12), residues: 1912 sheet: None (None), residues: 0 loop : -0.83 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 315 HIS 0.006 0.000 HIS D 172 PHE 0.029 0.001 PHE C 427 TYR 0.015 0.001 TYR A 524 ARG 0.003 0.000 ARG D 730 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4166.31 seconds wall clock time: 76 minutes 55.74 seconds (4615.74 seconds total)