Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 13:55:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/04_2023/5tqq_8435.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 8190 2.51 5 N 2048 2.21 5 O 2272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "L PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "M PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 39": "NH1" <-> "NH2" Residue "I GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12574 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4594 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4594 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 33, 'TRANS': 569} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "I" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 862 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 6.60, per 1000 atoms: 0.52 Number of scatterers: 12574 At special positions: 0 Unit cell: (102.7, 107.9, 141.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2272 8.00 N 2048 7.00 C 8190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.04 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: 5.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3044 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 16 sheets defined 56.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 49 through 86 removed outlier: 4.593A pdb=" N GLY A 86 " --> pdb=" O TYR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 removed outlier: 3.529A pdb=" N ARG A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.506A pdb=" N LEU A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.765A pdb=" N LEU A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.879A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.313A pdb=" N VAL A 149 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 193 through 214 Processing helix chain 'A' and resid 215 through 228 removed outlier: 3.527A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 253 Processing helix chain 'A' and resid 278 through 313 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 323 through 339 Processing helix chain 'A' and resid 340 through 349 removed outlier: 5.670A pdb=" N ARG A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.648A pdb=" N LEU A 358 " --> pdb=" O MET A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.886A pdb=" N PHE A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 419 removed outlier: 3.517A pdb=" N ILE A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 415 " --> pdb=" O TRP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 448 Processing helix chain 'A' and resid 462 through 480 removed outlier: 3.835A pdb=" N TYR A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 493 removed outlier: 3.801A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 516 removed outlier: 4.537A pdb=" N VAL A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 528 Processing helix chain 'A' and resid 546 through 551 removed outlier: 3.862A pdb=" N PHE A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 removed outlier: 3.590A pdb=" N VAL A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 670 through 682 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.944A pdb=" N LEU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.688A pdb=" N LYS H 65 " --> pdb=" O PRO H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 49 through 86 removed outlier: 4.593A pdb=" N GLY B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 3.530A pdb=" N ARG B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Proline residue: B 100 - end of helix removed outlier: 3.506A pdb=" N LEU B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.765A pdb=" N LEU B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.881A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.313A pdb=" N VAL B 149 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 188 Processing helix chain 'B' and resid 193 through 214 Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.525A pdb=" N GLY B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 221 " --> pdb=" O PHE B 217 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 253 Processing helix chain 'B' and resid 278 through 313 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 323 through 339 Processing helix chain 'B' and resid 340 through 349 removed outlier: 5.669A pdb=" N ARG B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.648A pdb=" N LEU B 358 " --> pdb=" O MET B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.886A pdb=" N PHE B 389 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 419 removed outlier: 3.517A pdb=" N ILE B 414 " --> pdb=" O PHE B 410 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 415 " --> pdb=" O TRP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 Processing helix chain 'B' and resid 462 through 480 removed outlier: 3.835A pdb=" N TYR B 466 " --> pdb=" O MET B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 removed outlier: 3.802A pdb=" N LEU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 516 removed outlier: 4.536A pdb=" N VAL B 501 " --> pdb=" O HIS B 497 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 528 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.863A pdb=" N PHE B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.589A pdb=" N VAL B 567 " --> pdb=" O PRO B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 605 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 670 through 682 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.944A pdb=" N LEU M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.689A pdb=" N LYS I 65 " --> pdb=" O PRO I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.654A pdb=" N LEU A 558 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR A 579 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A 593 " --> pdb=" O TYR A 579 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 581 " --> pdb=" O VAL A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 663 through 669 removed outlier: 5.787A pdb=" N ALA A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER A 660 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 666 " --> pdb=" O VAL A 658 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 633 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 659 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 635 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU B 633 " --> pdb=" O PHE B 657 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR B 659 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU B 635 " --> pdb=" O THR B 659 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 666 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 660 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.599A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.949A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 4.029A pdb=" N TRP L 50 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.534A pdb=" N GLN H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP H 73 " --> pdb=" O GLN H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR H 102 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 558 through 559 removed outlier: 6.655A pdb=" N LEU B 558 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR B 579 " --> pdb=" O THR B 593 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 593 " --> pdb=" O TYR B 579 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 581 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.598A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 10 through 13 removed outlier: 5.949A pdb=" N MET M 11 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR M 102 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR M 86 " --> pdb=" O THR M 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'M' and resid 53 through 54 removed outlier: 4.029A pdb=" N TRP M 50 " --> pdb=" O TYR M 53 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.534A pdb=" N GLN I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP I 73 " --> pdb=" O GLN I 78 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR I 102 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR I 51 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TRP I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2172 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: 4.00 Time building geometry restraints manager: 5.50 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: 2007 1.32 - 1.45: 3648 1.45 - 1.57: 7139 1.57 - 1.69: 8 1.69 - 1.81: 104 Bond restraints: 12906 Sorted by residual: bond pdb=" C PHE A 65 " pdb=" O PHE A 65 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.15e-02 7.56e+03 1.86e+01 bond pdb=" C PHE B 65 " pdb=" O PHE B 65 " ideal model delta sigma weight residual 1.236 1.286 -0.049 1.15e-02 7.56e+03 1.84e+01 bond pdb=" C GLN B 303 " pdb=" O GLN B 303 " ideal model delta sigma weight residual 1.236 1.282 -0.045 1.15e-02 7.56e+03 1.54e+01 bond pdb=" C GLN A 303 " pdb=" O GLN A 303 " ideal model delta sigma weight residual 1.236 1.282 -0.045 1.15e-02 7.56e+03 1.53e+01 bond pdb=" C GLY A 72 " pdb=" O GLY A 72 " ideal model delta sigma weight residual 1.234 1.273 -0.040 1.21e-02 6.83e+03 1.07e+01 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 462 106.81 - 113.62: 6785 113.62 - 120.42: 4796 120.42 - 127.22: 5382 127.22 - 134.02: 167 Bond angle restraints: 17592 Sorted by residual: angle pdb=" O LEU B 499 " pdb=" C LEU B 499 " pdb=" N PRO B 500 " ideal model delta sigma weight residual 120.27 125.66 -5.39 6.90e-01 2.10e+00 6.09e+01 angle pdb=" O LEU A 499 " pdb=" C LEU A 499 " pdb=" N PRO A 500 " ideal model delta sigma weight residual 120.27 125.56 -5.29 6.90e-01 2.10e+00 5.87e+01 angle pdb=" N ILE B 525 " pdb=" CA ILE B 525 " pdb=" CB ILE B 525 " ideal model delta sigma weight residual 110.55 119.08 -8.53 1.17e+00 7.31e-01 5.32e+01 angle pdb=" N ILE A 525 " pdb=" CA ILE A 525 " pdb=" CB ILE A 525 " ideal model delta sigma weight residual 110.55 119.06 -8.51 1.17e+00 7.31e-01 5.29e+01 angle pdb=" N PRO B 341 " pdb=" CA PRO B 341 " pdb=" C PRO B 341 " ideal model delta sigma weight residual 110.70 119.06 -8.36 1.22e+00 6.72e-01 4.70e+01 ... (remaining 17587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.61: 6619 13.61 - 27.22: 685 27.22 - 40.83: 154 40.83 - 54.44: 42 54.44 - 68.04: 12 Dihedral angle restraints: 7512 sinusoidal: 2776 harmonic: 4736 Sorted by residual: dihedral pdb=" C ILE B 511 " pdb=" N ILE B 511 " pdb=" CA ILE B 511 " pdb=" CB ILE B 511 " ideal model delta harmonic sigma weight residual -122.00 -140.23 18.23 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" C ILE A 511 " pdb=" N ILE A 511 " pdb=" CA ILE A 511 " pdb=" CB ILE A 511 " ideal model delta harmonic sigma weight residual -122.00 -140.16 18.16 0 2.50e+00 1.60e-01 5.28e+01 dihedral pdb=" C THR A 417 " pdb=" N THR A 417 " pdb=" CA THR A 417 " pdb=" CB THR A 417 " ideal model delta harmonic sigma weight residual -122.00 -137.75 15.75 0 2.50e+00 1.60e-01 3.97e+01 ... (remaining 7509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1763 0.122 - 0.243: 217 0.243 - 0.365: 38 0.365 - 0.486: 8 0.486 - 0.608: 6 Chirality restraints: 2032 Sorted by residual: chirality pdb=" CA ILE B 511 " pdb=" N ILE B 511 " pdb=" C ILE B 511 " pdb=" CB ILE B 511 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" CA ILE A 511 " pdb=" N ILE A 511 " pdb=" C ILE A 511 " pdb=" CB ILE A 511 " both_signs ideal model delta sigma weight residual False 2.43 1.83 0.60 2.00e-01 2.50e+01 9.09e+00 chirality pdb=" CA THR A 417 " pdb=" N THR A 417 " pdb=" C THR A 417 " pdb=" CB THR A 417 " both_signs ideal model delta sigma weight residual False 2.53 1.94 0.59 2.00e-01 2.50e+01 8.66e+00 ... (remaining 2029 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 101 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C VAL B 101 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 101 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA B 102 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 101 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.37e+01 pdb=" C VAL A 101 " 0.064 2.00e-02 2.50e+03 pdb=" O VAL A 101 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 102 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 412 " 0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C MET B 412 " -0.063 2.00e-02 2.50e+03 pdb=" O MET B 412 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 413 " 0.022 2.00e-02 2.50e+03 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 124 2.69 - 3.24: 13047 3.24 - 3.79: 19495 3.79 - 4.35: 25730 4.35 - 4.90: 42283 Nonbonded interactions: 100679 Sorted by model distance: nonbonded pdb=" O ALA A 471 " pdb=" OG SER A 475 " model vdw 2.136 2.440 nonbonded pdb=" O ALA B 471 " pdb=" OG SER B 475 " model vdw 2.137 2.440 nonbonded pdb=" O ALA A 368 " pdb=" OG1 THR A 371 " model vdw 2.360 2.440 nonbonded pdb=" O ALA B 368 " pdb=" OG1 THR B 371 " model vdw 2.361 2.440 nonbonded pdb=" O LEU B 335 " pdb=" OG1 THR B 339 " model vdw 2.395 2.440 ... (remaining 100674 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' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 4.300 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.110 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.008 0.056 12906 Z= 0.539 Angle : 1.517 8.531 17592 Z= 1.142 Chirality : 0.093 0.608 2032 Planarity : 0.006 0.082 2188 Dihedral : 12.216 68.044 4456 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.70 % Favored : 95.18 % Rotamer Outliers : 0.89 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 4.88 % 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: -0.21 (0.18), residues: 1618 helix: 1.65 (0.14), residues: 794 sheet: -1.34 (0.36), residues: 172 loop : -2.17 (0.21), residues: 652 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 316 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 320 average time/residue: 0.2528 time to fit residues: 115.1629 Evaluate side-chains 156 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1681 time to fit residues: 2.5557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 126 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS L 32 ASN B 78 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS M 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12906 Z= 0.209 Angle : 0.625 6.769 17592 Z= 0.315 Chirality : 0.041 0.167 2032 Planarity : 0.005 0.051 2188 Dihedral : 4.511 21.341 1748 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.61 (0.22), residues: 1618 helix: 3.51 (0.18), residues: 812 sheet: -1.45 (0.32), residues: 210 loop : -1.62 (0.23), residues: 596 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 205 average time/residue: 0.2557 time to fit residues: 76.0047 Evaluate side-chains 153 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.497 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1201 time to fit residues: 5.3323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 12906 Z= 0.273 Angle : 0.587 6.321 17592 Z= 0.298 Chirality : 0.039 0.151 2032 Planarity : 0.005 0.047 2188 Dihedral : 4.273 18.973 1748 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.43 (0.22), residues: 1618 helix: 3.19 (0.18), residues: 808 sheet: -1.45 (0.32), residues: 212 loop : -1.40 (0.23), residues: 598 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 160 average time/residue: 0.2432 time to fit residues: 57.9196 Evaluate side-chains 140 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1198 time to fit residues: 3.6602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS L 89 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12906 Z= 0.221 Angle : 0.556 5.967 17592 Z= 0.282 Chirality : 0.039 0.152 2032 Planarity : 0.004 0.038 2188 Dihedral : 4.135 17.495 1748 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.41 (0.22), residues: 1618 helix: 3.01 (0.19), residues: 808 sheet: -1.36 (0.33), residues: 212 loop : -1.19 (0.24), residues: 598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 172 average time/residue: 0.2189 time to fit residues: 57.5472 Evaluate side-chains 138 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.441 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1192 time to fit residues: 3.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 HIS L 89 GLN B 198 ASN B 549 HIS M 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 12906 Z= 0.308 Angle : 0.593 6.796 17592 Z= 0.303 Chirality : 0.039 0.157 2032 Planarity : 0.004 0.039 2188 Dihedral : 4.296 17.717 1748 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.35 (0.22), residues: 1618 helix: 2.72 (0.18), residues: 816 sheet: -1.39 (0.33), residues: 212 loop : -0.87 (0.25), residues: 590 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 149 average time/residue: 0.2334 time to fit residues: 52.4307 Evaluate side-chains 127 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1245 time to fit residues: 3.8028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 497 HIS M 27 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 12906 Z= 0.255 Angle : 0.588 7.144 17592 Z= 0.295 Chirality : 0.039 0.161 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.207 17.593 1748 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.38 (0.22), residues: 1618 helix: 2.69 (0.18), residues: 808 sheet: -1.27 (0.32), residues: 214 loop : -0.75 (0.26), residues: 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 148 average time/residue: 0.2378 time to fit residues: 52.8838 Evaluate side-chains 130 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1263 time to fit residues: 4.4260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS M 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 12906 Z= 0.209 Angle : 0.578 8.119 17592 Z= 0.291 Chirality : 0.040 0.184 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.094 16.806 1748 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.42 (0.22), residues: 1618 helix: 2.73 (0.18), residues: 808 sheet: -1.22 (0.32), residues: 212 loop : -0.76 (0.26), residues: 598 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.514 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 141 average time/residue: 0.2305 time to fit residues: 49.4835 Evaluate side-chains 126 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1258 time to fit residues: 3.0846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 12906 Z= 0.368 Angle : 0.670 8.701 17592 Z= 0.338 Chirality : 0.041 0.164 2032 Planarity : 0.005 0.051 2188 Dihedral : 4.421 18.072 1748 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.17 (0.21), residues: 1618 helix: 2.36 (0.18), residues: 820 sheet: -0.93 (0.33), residues: 202 loop : -0.88 (0.25), residues: 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.2423 time to fit residues: 46.1776 Evaluate side-chains 126 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.353 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1315 time to fit residues: 4.4717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12906 Z= 0.187 Angle : 0.596 8.275 17592 Z= 0.297 Chirality : 0.040 0.175 2032 Planarity : 0.004 0.044 2188 Dihedral : 4.116 16.923 1748 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.41 (0.21), residues: 1618 helix: 2.61 (0.18), residues: 812 sheet: -0.66 (0.34), residues: 202 loop : -0.86 (0.25), residues: 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 141 average time/residue: 0.2347 time to fit residues: 49.9472 Evaluate side-chains 126 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1256 time to fit residues: 3.3797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 148 optimal weight: 0.0170 chunk 128 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12906 Z= 0.180 Angle : 0.620 10.250 17592 Z= 0.307 Chirality : 0.039 0.184 2032 Planarity : 0.004 0.044 2188 Dihedral : 4.014 16.070 1748 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.55 (0.22), residues: 1618 helix: 2.64 (0.18), residues: 814 sheet: -0.31 (0.34), residues: 210 loop : -0.79 (0.25), residues: 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3236 Ramachandran restraints generated. 1618 Oldfield, 0 Emsley, 1618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 135 average time/residue: 0.2706 time to fit residues: 53.5537 Evaluate side-chains 129 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1336 time to fit residues: 2.3145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.046121 restraints weight = 60748.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.047636 restraints weight = 28064.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.048682 restraints weight = 16763.458| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12906 Z= 0.183 Angle : 0.611 9.138 17592 Z= 0.304 Chirality : 0.040 0.168 2032 Planarity : 0.004 0.044 2188 Dihedral : 3.970 16.699 1748 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.58 (0.22), residues: 1618 helix: 2.58 (0.18), residues: 830 sheet: -0.21 (0.36), residues: 202 loop : -0.78 (0.25), residues: 586 =============================================================================== Job complete usr+sys time: 2138.03 seconds wall clock time: 40 minutes 20.84 seconds (2420.84 seconds total)