Starting phenix.real_space_refine on Thu Feb 15 14:47:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/02_2024/5tqq_8435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/02_2024/5tqq_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_8435/02_2024/5tqq_8435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/02_2024/5tqq_8435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/02_2024/5tqq_8435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tqq_8435/02_2024/5tqq_8435.pdb" } resolution = 3.76 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= 0.003 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-dev-5238/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: 7.13, per 1000 atoms: 0.57 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 2.3 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: 1.34 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: 4.33 Time building geometry restraints manager: 5.54 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: 0.730 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: 3.640 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.340 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- 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 % Allowed : 5.36 % Favored : 93.75 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 411 HIS 0.009 0.002 HIS B 497 PHE 0.027 0.003 PHE A 410 TYR 0.022 0.002 TYR B 138 ARG 0.007 0.001 ARG H 98 *********************** 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 : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8072 (t0) cc_final: 0.7651 (t70) REVERT: A 217 PHE cc_start: 0.8162 (m-80) cc_final: 0.7929 (m-80) REVERT: A 240 PHE cc_start: 0.8316 (t80) cc_final: 0.7950 (t80) REVERT: A 363 ASP cc_start: 0.7855 (t0) cc_final: 0.7620 (t0) REVERT: A 412 MET cc_start: 0.8739 (mtp) cc_final: 0.8518 (mtt) REVERT: A 551 MET cc_start: 0.9198 (ptm) cc_final: 0.8855 (ptt) REVERT: L 17 ASP cc_start: 0.8361 (m-30) cc_final: 0.8112 (m-30) REVERT: L 39 LYS cc_start: 0.9131 (mttt) cc_final: 0.8899 (mmmt) REVERT: L 55 TYR cc_start: 0.8558 (t80) cc_final: 0.7595 (t80) REVERT: L 61 ARG cc_start: 0.7784 (ptt90) cc_final: 0.7164 (ptt90) REVERT: L 77 ASN cc_start: 0.9339 (m-40) cc_final: 0.8954 (t0) REVERT: L 79 GLN cc_start: 0.9071 (mt0) cc_final: 0.8639 (mp10) REVERT: L 83 LEU cc_start: 0.8755 (mt) cc_final: 0.8528 (mm) REVERT: H 32 ASP cc_start: 0.8662 (t0) cc_final: 0.8057 (m-30) REVERT: H 33 TYR cc_start: 0.7983 (m-80) cc_final: 0.7739 (m-80) REVERT: H 47 GLU cc_start: 0.8585 (tt0) cc_final: 0.8074 (tt0) REVERT: H 49 MET cc_start: 0.8955 (mmm) cc_final: 0.8338 (mmm) REVERT: H 67 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8161 (mtm180) REVERT: H 82 GLN cc_start: 0.8919 (mt0) cc_final: 0.8558 (mp10) REVERT: H 101 ASP cc_start: 0.9081 (m-30) cc_final: 0.8848 (m-30) REVERT: B 140 ASP cc_start: 0.8069 (t0) cc_final: 0.7654 (t70) REVERT: B 217 PHE cc_start: 0.8193 (m-80) cc_final: 0.7925 (m-80) REVERT: B 240 PHE cc_start: 0.8313 (t80) cc_final: 0.7907 (t80) REVERT: B 359 ASP cc_start: 0.8834 (m-30) cc_final: 0.8608 (m-30) REVERT: B 363 ASP cc_start: 0.7855 (t0) cc_final: 0.7622 (t0) REVERT: B 412 MET cc_start: 0.8732 (mtp) cc_final: 0.8522 (mtt) REVERT: B 551 MET cc_start: 0.9190 (ptm) cc_final: 0.8854 (ptt) REVERT: M 17 ASP cc_start: 0.8359 (m-30) cc_final: 0.8110 (m-30) REVERT: M 39 LYS cc_start: 0.9128 (mttt) cc_final: 0.8901 (mmmt) REVERT: M 55 TYR cc_start: 0.8552 (t80) cc_final: 0.7499 (t80) REVERT: M 61 ARG cc_start: 0.7754 (ptt90) cc_final: 0.7138 (ptt90) REVERT: M 77 ASN cc_start: 0.9335 (m-40) cc_final: 0.8953 (t0) REVERT: M 79 GLN cc_start: 0.9067 (mt0) cc_final: 0.8642 (mp10) REVERT: M 83 LEU cc_start: 0.8768 (mt) cc_final: 0.8542 (mm) REVERT: I 32 ASP cc_start: 0.8660 (t0) cc_final: 0.8073 (m-30) REVERT: I 33 TYR cc_start: 0.8000 (m-80) cc_final: 0.7757 (m-80) REVERT: I 47 GLU cc_start: 0.8588 (tt0) cc_final: 0.8074 (tt0) REVERT: I 49 MET cc_start: 0.8946 (mmm) cc_final: 0.8336 (mmm) REVERT: I 67 ARG cc_start: 0.8664 (ptp-170) cc_final: 0.8166 (mtm180) REVERT: I 82 GLN cc_start: 0.8915 (mt0) cc_final: 0.8554 (mp10) REVERT: I 101 ASP cc_start: 0.9068 (m-30) cc_final: 0.8828 (m-30) outliers start: 12 outliers final: 2 residues processed: 320 average time/residue: 0.2521 time to fit residues: 114.9264 Evaluate side-chains 179 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain M residue 49 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 386 ASN A 480 HIS L 32 ASN B 78 HIS ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN B 480 HIS M 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12906 Z= 0.197 Angle : 0.616 7.163 17592 Z= 0.308 Chirality : 0.041 0.159 2032 Planarity : 0.005 0.050 2188 Dihedral : 4.766 45.321 1752 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.68 % Allowed : 12.28 % Favored : 85.04 % 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: 1.64 (0.22), residues: 1618 helix: 3.57 (0.18), residues: 808 sheet: -1.49 (0.32), residues: 210 loop : -1.59 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.004 0.001 HIS B 497 PHE 0.020 0.002 PHE B 52 TYR 0.013 0.001 TYR A 236 ARG 0.004 0.000 ARG A 182 *********************** 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 227 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 191 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.8352 (t80) cc_final: 0.7984 (t80) REVERT: A 354 MET cc_start: 0.8846 (mmm) cc_final: 0.8578 (mmt) REVERT: A 503 MET cc_start: 0.9006 (ttm) cc_final: 0.8451 (mtm) REVERT: A 551 MET cc_start: 0.9162 (ptm) cc_final: 0.8661 (ptt) REVERT: L 4 MET cc_start: 0.8050 (mmm) cc_final: 0.7038 (mmm) REVERT: L 6 GLN cc_start: 0.7956 (pm20) cc_final: 0.7582 (pm20) REVERT: L 11 MET cc_start: 0.8965 (mtp) cc_final: 0.8652 (mpp) REVERT: L 17 ASP cc_start: 0.8323 (m-30) cc_final: 0.8075 (m-30) REVERT: L 39 LYS cc_start: 0.9121 (mttt) cc_final: 0.8885 (mmmm) REVERT: L 55 TYR cc_start: 0.8566 (t80) cc_final: 0.7752 (t80) REVERT: L 77 ASN cc_start: 0.9333 (m-40) cc_final: 0.8871 (t0) REVERT: L 83 LEU cc_start: 0.8725 (mt) cc_final: 0.8432 (mm) REVERT: H 32 ASP cc_start: 0.8710 (t0) cc_final: 0.8008 (m-30) REVERT: H 47 GLU cc_start: 0.8472 (tt0) cc_final: 0.8001 (tt0) REVERT: H 49 MET cc_start: 0.8938 (mmm) cc_final: 0.8484 (mmm) REVERT: H 73 ASP cc_start: 0.8014 (t0) cc_final: 0.7757 (t0) REVERT: B 240 PHE cc_start: 0.8349 (t80) cc_final: 0.7968 (t80) REVERT: B 328 SER cc_start: 0.9439 (t) cc_final: 0.9204 (p) REVERT: B 355 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7534 (tpt170) REVERT: B 356 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8754 (mt-10) REVERT: B 359 ASP cc_start: 0.8708 (m-30) cc_final: 0.8507 (m-30) REVERT: B 363 ASP cc_start: 0.7590 (t0) cc_final: 0.7368 (t0) REVERT: B 503 MET cc_start: 0.9034 (ttm) cc_final: 0.8559 (mtm) REVERT: B 551 MET cc_start: 0.9161 (ptm) cc_final: 0.8667 (ptt) REVERT: M 4 MET cc_start: 0.7996 (mmm) cc_final: 0.6882 (mmm) REVERT: M 6 GLN cc_start: 0.7959 (pm20) cc_final: 0.7570 (pm20) REVERT: M 11 MET cc_start: 0.8963 (mtp) cc_final: 0.8654 (mpp) REVERT: M 17 ASP cc_start: 0.8219 (m-30) cc_final: 0.7996 (m-30) REVERT: M 39 LYS cc_start: 0.9091 (mttt) cc_final: 0.8836 (mmmt) REVERT: M 55 TYR cc_start: 0.8562 (t80) cc_final: 0.7727 (t80) REVERT: M 77 ASN cc_start: 0.9331 (m-40) cc_final: 0.8868 (t0) REVERT: M 83 LEU cc_start: 0.8740 (mt) cc_final: 0.8504 (mm) REVERT: I 32 ASP cc_start: 0.8673 (t0) cc_final: 0.8037 (m-30) REVERT: I 47 GLU cc_start: 0.8473 (tt0) cc_final: 0.7965 (tt0) REVERT: I 49 MET cc_start: 0.8934 (mmm) cc_final: 0.8457 (mmm) REVERT: I 73 ASP cc_start: 0.8023 (t0) cc_final: 0.7756 (t0) REVERT: I 101 ASP cc_start: 0.9081 (m-30) cc_final: 0.8875 (m-30) outliers start: 36 outliers final: 13 residues processed: 217 average time/residue: 0.2460 time to fit residues: 76.9528 Evaluate side-chains 172 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 159 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain I residue 109 VAL 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: 0.0470 chunk 122 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 147 optimal weight: 0.0060 chunk 159 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 overall best weight: 0.7698 ------------------------------------------------------------------------------- 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** H 78 GLN H 82 GLN B 198 ASN I 78 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3264 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= 0.174 Angle : 0.551 6.081 17592 Z= 0.276 Chirality : 0.039 0.150 2032 Planarity : 0.004 0.045 2188 Dihedral : 4.352 45.194 1752 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.19 % Allowed : 15.77 % Favored : 83.04 % 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: 1.69 (0.22), residues: 1618 helix: 3.46 (0.18), residues: 808 sheet: -1.26 (0.33), residues: 210 loop : -1.40 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 50 HIS 0.002 0.000 HIS A 497 PHE 0.015 0.001 PHE A 52 TYR 0.020 0.001 TYR I 33 ARG 0.002 0.000 ARG A 182 *********************** 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 194 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 PHE cc_start: 0.8360 (t80) cc_final: 0.7930 (t80) REVERT: A 359 ASP cc_start: 0.8878 (t0) cc_final: 0.8562 (m-30) REVERT: A 363 ASP cc_start: 0.7877 (t0) cc_final: 0.7651 (t0) REVERT: A 503 MET cc_start: 0.9082 (ttm) cc_final: 0.8431 (mtp) REVERT: A 551 MET cc_start: 0.9195 (ptm) cc_final: 0.8665 (ptt) REVERT: A 576 MET cc_start: 0.7214 (mmm) cc_final: 0.6983 (mmm) REVERT: L 4 MET cc_start: 0.7935 (mmm) cc_final: 0.6924 (mmm) REVERT: L 6 GLN cc_start: 0.7990 (pm20) cc_final: 0.7732 (pm20) REVERT: L 17 ASP cc_start: 0.8046 (m-30) cc_final: 0.7841 (m-30) REVERT: L 39 LYS cc_start: 0.9146 (mttt) cc_final: 0.8911 (mmmm) REVERT: L 55 TYR cc_start: 0.8417 (t80) cc_final: 0.8105 (t80) REVERT: L 77 ASN cc_start: 0.9333 (m-40) cc_final: 0.9115 (t0) REVERT: L 83 LEU cc_start: 0.8687 (mt) cc_final: 0.8353 (mm) REVERT: H 47 GLU cc_start: 0.8374 (tt0) cc_final: 0.7979 (tt0) REVERT: H 49 MET cc_start: 0.8843 (mmm) cc_final: 0.8418 (mpp) REVERT: B 231 PHE cc_start: 0.8292 (m-80) cc_final: 0.8067 (m-80) REVERT: B 240 PHE cc_start: 0.8357 (t80) cc_final: 0.7904 (t80) REVERT: B 354 MET cc_start: 0.8529 (tpp) cc_final: 0.8185 (mmt) REVERT: B 355 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7786 (tpt170) REVERT: B 356 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8723 (mt-10) REVERT: B 363 ASP cc_start: 0.7497 (t0) cc_final: 0.7268 (t0) REVERT: B 503 MET cc_start: 0.9016 (ttm) cc_final: 0.8387 (mtp) REVERT: B 551 MET cc_start: 0.9172 (ptm) cc_final: 0.8674 (ptt) REVERT: B 576 MET cc_start: 0.7208 (mmm) cc_final: 0.6981 (mmm) REVERT: M 4 MET cc_start: 0.7941 (mmm) cc_final: 0.6897 (mmm) REVERT: M 6 GLN cc_start: 0.7992 (pm20) cc_final: 0.7727 (pm20) REVERT: M 17 ASP cc_start: 0.8041 (m-30) cc_final: 0.7835 (m-30) REVERT: M 39 LYS cc_start: 0.9112 (mttt) cc_final: 0.8863 (mmmm) REVERT: M 55 TYR cc_start: 0.8504 (t80) cc_final: 0.7526 (t80) REVERT: M 77 ASN cc_start: 0.9330 (m-40) cc_final: 0.9115 (t0) REVERT: M 83 LEU cc_start: 0.8708 (mt) cc_final: 0.8429 (mm) REVERT: I 47 GLU cc_start: 0.8376 (tt0) cc_final: 0.7979 (tt0) REVERT: I 49 MET cc_start: 0.8874 (mmm) cc_final: 0.8474 (mpp) REVERT: I 101 ASP cc_start: 0.9060 (m-30) cc_final: 0.8772 (m-30) outliers start: 16 outliers final: 9 residues processed: 186 average time/residue: 0.2372 time to fit residues: 64.7077 Evaluate side-chains 162 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 60 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 A 652 ASN L 89 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 HIS B 652 ASN M 89 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12906 Z= 0.251 Angle : 0.554 6.070 17592 Z= 0.281 Chirality : 0.039 0.169 2032 Planarity : 0.004 0.038 2188 Dihedral : 4.334 41.636 1752 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.12 % Allowed : 16.82 % Favored : 80.06 % 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: 1.53 (0.22), residues: 1618 helix: 3.10 (0.18), residues: 810 sheet: -1.18 (0.34), residues: 210 loop : -1.17 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 391 HIS 0.003 0.001 HIS A 393 PHE 0.020 0.002 PHE I 79 TYR 0.022 0.002 TYR I 33 ARG 0.001 0.000 ARG B 595 *********************** 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 193 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8878 (t0) cc_final: 0.8554 (m-30) REVERT: A 408 MET cc_start: 0.8610 (mmp) cc_final: 0.8214 (mmp) REVERT: A 412 MET cc_start: 0.8769 (mtt) cc_final: 0.8558 (mtm) REVERT: A 551 MET cc_start: 0.9252 (ptm) cc_final: 0.8878 (ptt) REVERT: L 4 MET cc_start: 0.7525 (mmm) cc_final: 0.6250 (tmm) REVERT: L 6 GLN cc_start: 0.7838 (pm20) cc_final: 0.7556 (pm20) REVERT: L 39 LYS cc_start: 0.9124 (mttt) cc_final: 0.8873 (mmmm) REVERT: L 83 LEU cc_start: 0.8700 (mt) cc_final: 0.8456 (mm) REVERT: H 47 GLU cc_start: 0.8330 (tt0) cc_final: 0.7781 (tt0) REVERT: H 49 MET cc_start: 0.8957 (mmm) cc_final: 0.8598 (mmm) REVERT: H 82 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7274 (mp10) REVERT: B 355 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7828 (tpt170) REVERT: B 356 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8733 (mt-10) REVERT: B 363 ASP cc_start: 0.7653 (t0) cc_final: 0.7304 (t0) REVERT: B 408 MET cc_start: 0.8626 (mmp) cc_final: 0.8247 (mmp) REVERT: B 503 MET cc_start: 0.9048 (ttm) cc_final: 0.8232 (mtp) REVERT: B 551 MET cc_start: 0.9247 (ptm) cc_final: 0.8875 (ptt) REVERT: M 4 MET cc_start: 0.7804 (mmm) cc_final: 0.7086 (mmm) REVERT: M 39 LYS cc_start: 0.9123 (mttt) cc_final: 0.8874 (mmmm) REVERT: M 55 TYR cc_start: 0.8470 (t80) cc_final: 0.7606 (t80) REVERT: M 83 LEU cc_start: 0.8708 (mt) cc_final: 0.8464 (mm) REVERT: I 27 ASP cc_start: 0.6560 (t0) cc_final: 0.6116 (t0) REVERT: I 47 GLU cc_start: 0.8331 (tt0) cc_final: 0.7779 (tt0) REVERT: I 49 MET cc_start: 0.8948 (mmm) cc_final: 0.8595 (mmm) REVERT: I 101 ASP cc_start: 0.9094 (m-30) cc_final: 0.8812 (m-30) outliers start: 42 outliers final: 27 residues processed: 182 average time/residue: 0.2234 time to fit residues: 60.1207 Evaluate side-chains 164 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 137 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 133 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN B 549 HIS ** I 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3994 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= 0.186 Angle : 0.538 7.558 17592 Z= 0.269 Chirality : 0.038 0.163 2032 Planarity : 0.004 0.039 2188 Dihedral : 4.245 41.894 1752 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.31 % Allowed : 18.23 % Favored : 79.46 % 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: 1.65 (0.22), residues: 1618 helix: 3.06 (0.18), residues: 810 sheet: -0.95 (0.34), residues: 210 loop : -0.97 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 411 HIS 0.003 0.001 HIS B 393 PHE 0.021 0.001 PHE B 213 TYR 0.021 0.001 TYR I 33 ARG 0.002 0.000 ARG A 595 *********************** 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 194 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 359 ASP cc_start: 0.8869 (t0) cc_final: 0.8541 (m-30) REVERT: A 408 MET cc_start: 0.8359 (mmp) cc_final: 0.8080 (mmp) REVERT: A 412 MET cc_start: 0.8780 (mtt) cc_final: 0.8568 (mtm) REVERT: A 479 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 503 MET cc_start: 0.9061 (ttm) cc_final: 0.8328 (mtp) REVERT: A 551 MET cc_start: 0.9098 (ptm) cc_final: 0.8641 (ptt) REVERT: L 4 MET cc_start: 0.7443 (mmm) cc_final: 0.6519 (mmm) REVERT: L 6 GLN cc_start: 0.7811 (pm20) cc_final: 0.7551 (pm20) REVERT: L 9 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7911 (tptp) REVERT: L 11 MET cc_start: 0.8569 (mtp) cc_final: 0.8180 (mpp) REVERT: L 39 LYS cc_start: 0.9164 (mttt) cc_final: 0.8904 (mmmm) REVERT: L 83 LEU cc_start: 0.8681 (mt) cc_final: 0.8260 (mm) REVERT: L 89 GLN cc_start: 0.8847 (tt0) cc_final: 0.8457 (tt0) REVERT: H 5 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: H 27 ASP cc_start: 0.6436 (t0) cc_final: 0.6032 (t0) REVERT: H 47 GLU cc_start: 0.8276 (tt0) cc_final: 0.7842 (tt0) REVERT: H 49 MET cc_start: 0.8856 (mmm) cc_final: 0.8335 (mpp) REVERT: H 82 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7373 (mp10) REVERT: B 231 PHE cc_start: 0.8044 (m-80) cc_final: 0.7827 (m-80) REVERT: B 250 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7873 (m-80) REVERT: B 355 ARG cc_start: 0.8044 (ttm110) cc_final: 0.7842 (tpt170) REVERT: B 356 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8727 (mp0) REVERT: B 363 ASP cc_start: 0.7657 (t0) cc_final: 0.7346 (t0) REVERT: B 479 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (p) REVERT: B 503 MET cc_start: 0.9010 (ttm) cc_final: 0.8326 (mtp) REVERT: B 551 MET cc_start: 0.9256 (ptm) cc_final: 0.8691 (ptt) REVERT: M 4 MET cc_start: 0.7533 (mmm) cc_final: 0.6733 (tmm) REVERT: M 9 LYS cc_start: 0.8410 (mmmm) cc_final: 0.7933 (tptp) REVERT: M 39 LYS cc_start: 0.9162 (mttt) cc_final: 0.8892 (mmmm) REVERT: M 83 LEU cc_start: 0.8682 (mt) cc_final: 0.8269 (mm) REVERT: M 89 GLN cc_start: 0.8871 (tt0) cc_final: 0.8520 (tt0) REVERT: I 27 ASP cc_start: 0.6630 (t0) cc_final: 0.6136 (t0) REVERT: I 47 GLU cc_start: 0.8280 (tt0) cc_final: 0.7845 (tt0) REVERT: I 49 MET cc_start: 0.8896 (mmm) cc_final: 0.8341 (mpp) REVERT: I 82 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7235 (mp10) REVERT: I 101 ASP cc_start: 0.9055 (m-30) cc_final: 0.8800 (m-30) outliers start: 31 outliers final: 17 residues processed: 185 average time/residue: 0.2373 time to fit residues: 65.1676 Evaluate side-chains 165 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12906 Z= 0.242 Angle : 0.566 7.431 17592 Z= 0.283 Chirality : 0.039 0.167 2032 Planarity : 0.004 0.039 2188 Dihedral : 4.251 39.873 1752 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.20 % Allowed : 17.93 % Favored : 78.87 % 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: 1.64 (0.22), residues: 1618 helix: 2.89 (0.18), residues: 814 sheet: -0.81 (0.34), residues: 210 loop : -0.81 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 234 HIS 0.003 0.001 HIS B 364 PHE 0.025 0.002 PHE A 213 TYR 0.019 0.002 TYR I 33 ARG 0.002 0.000 ARG H 98 *********************** 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 186 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: A 359 ASP cc_start: 0.8878 (t0) cc_final: 0.8557 (m-30) REVERT: A 408 MET cc_start: 0.8377 (mmp) cc_final: 0.8088 (mmp) REVERT: A 412 MET cc_start: 0.8752 (mtt) cc_final: 0.8543 (mtm) REVERT: A 479 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 551 MET cc_start: 0.9145 (ptm) cc_final: 0.8688 (ptt) REVERT: L 4 MET cc_start: 0.7445 (mmm) cc_final: 0.6448 (mmm) REVERT: L 39 LYS cc_start: 0.9129 (mttt) cc_final: 0.8901 (mmmm) REVERT: L 89 GLN cc_start: 0.8879 (tt0) cc_final: 0.8529 (tt0) REVERT: H 5 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: H 27 ASP cc_start: 0.6381 (t0) cc_final: 0.5908 (t0) REVERT: H 47 GLU cc_start: 0.8378 (tt0) cc_final: 0.7817 (tt0) REVERT: H 49 MET cc_start: 0.8861 (mmm) cc_final: 0.8556 (mmm) REVERT: B 231 PHE cc_start: 0.8194 (m-80) cc_final: 0.7989 (m-80) REVERT: B 250 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: B 356 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8684 (mp0) REVERT: B 479 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 551 MET cc_start: 0.9139 (ptm) cc_final: 0.8687 (ptt) REVERT: M 4 MET cc_start: 0.7454 (mmm) cc_final: 0.6915 (mmm) REVERT: M 9 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7807 (tptp) REVERT: M 11 MET cc_start: 0.8875 (mtp) cc_final: 0.8634 (mpp) REVERT: M 39 LYS cc_start: 0.9104 (mttt) cc_final: 0.8810 (mmmm) REVERT: M 83 LEU cc_start: 0.8716 (mt) cc_final: 0.8370 (mm) REVERT: M 89 GLN cc_start: 0.8832 (tt0) cc_final: 0.8474 (tt0) REVERT: I 27 ASP cc_start: 0.7081 (t0) cc_final: 0.6617 (t0) REVERT: I 47 GLU cc_start: 0.8381 (tt0) cc_final: 0.7932 (tt0) REVERT: I 49 MET cc_start: 0.8866 (mmm) cc_final: 0.8308 (mpp) outliers start: 43 outliers final: 27 residues processed: 173 average time/residue: 0.2362 time to fit residues: 60.6605 Evaluate side-chains 165 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.0050 chunk 114 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 156 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 overall best weight: 0.4172 ------------------------------------------------------------------------------- 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 ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12906 Z= 0.158 Angle : 0.548 7.461 17592 Z= 0.270 Chirality : 0.039 0.191 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.036 40.220 1752 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.31 % Allowed : 19.35 % Favored : 78.35 % 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: 1.73 (0.22), residues: 1618 helix: 2.92 (0.18), residues: 816 sheet: -0.52 (0.35), residues: 206 loop : -0.82 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.002 0.000 HIS B 393 PHE 0.015 0.001 PHE A 213 TYR 0.017 0.001 TYR I 33 ARG 0.002 0.000 ARG M 54 *********************** 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 192 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: A 359 ASP cc_start: 0.8892 (t0) cc_final: 0.8561 (m-30) REVERT: A 479 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8932 (p) REVERT: A 551 MET cc_start: 0.8983 (ptm) cc_final: 0.8601 (ptt) REVERT: L 4 MET cc_start: 0.7107 (mmm) cc_final: 0.6469 (mmm) REVERT: L 11 MET cc_start: 0.8782 (mtp) cc_final: 0.8345 (mpp) REVERT: L 39 LYS cc_start: 0.9114 (mttt) cc_final: 0.8907 (mmmm) REVERT: L 83 LEU cc_start: 0.8993 (mm) cc_final: 0.8532 (mm) REVERT: L 89 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: H 5 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8715 (mp10) REVERT: H 27 ASP cc_start: 0.6418 (t0) cc_final: 0.5952 (t0) REVERT: H 47 GLU cc_start: 0.8398 (tt0) cc_final: 0.7990 (tt0) REVERT: H 49 MET cc_start: 0.8799 (mmm) cc_final: 0.8297 (mpp) REVERT: H 82 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7050 (mp10) REVERT: B 250 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7779 (m-80) REVERT: B 354 MET cc_start: 0.8760 (mmm) cc_final: 0.8547 (mmt) REVERT: B 356 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8673 (mp0) REVERT: B 479 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8912 (p) REVERT: B 551 MET cc_start: 0.8976 (ptm) cc_final: 0.8598 (ptt) REVERT: M 4 MET cc_start: 0.7573 (mmm) cc_final: 0.6688 (tmm) REVERT: M 39 LYS cc_start: 0.9112 (mttt) cc_final: 0.8861 (mmmm) REVERT: M 83 LEU cc_start: 0.8676 (mt) cc_final: 0.8395 (mm) REVERT: M 89 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: I 5 GLN cc_start: 0.9164 (tp40) cc_final: 0.8822 (mm110) REVERT: I 27 ASP cc_start: 0.7325 (t0) cc_final: 0.6945 (t0) REVERT: I 47 GLU cc_start: 0.8409 (tt0) cc_final: 0.8000 (tt0) REVERT: I 49 MET cc_start: 0.8802 (mmm) cc_final: 0.8303 (mpp) REVERT: I 82 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7065 (mp10) outliers start: 31 outliers final: 18 residues processed: 183 average time/residue: 0.2315 time to fit residues: 62.8628 Evaluate side-chains 164 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.4524 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= 0.215 Angle : 0.573 8.461 17592 Z= 0.282 Chirality : 0.039 0.164 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.048 36.261 1752 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.53 % Allowed : 19.94 % Favored : 77.53 % 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: 1.73 (0.22), residues: 1618 helix: 2.92 (0.18), residues: 816 sheet: -0.57 (0.35), residues: 206 loop : -0.80 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 411 HIS 0.003 0.001 HIS B 171 PHE 0.016 0.001 PHE A 213 TYR 0.018 0.001 TYR I 33 ARG 0.002 0.000 ARG M 18 *********************** 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 172 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: A 359 ASP cc_start: 0.8903 (t0) cc_final: 0.8562 (m-30) REVERT: A 479 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8921 (p) REVERT: A 551 MET cc_start: 0.9048 (ptm) cc_final: 0.8670 (ptt) REVERT: L 4 MET cc_start: 0.7162 (mmm) cc_final: 0.6586 (mmm) REVERT: L 39 LYS cc_start: 0.9058 (mttt) cc_final: 0.8838 (mmmm) REVERT: L 89 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: H 5 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: H 27 ASP cc_start: 0.6836 (t0) cc_final: 0.6418 (t0) REVERT: H 47 GLU cc_start: 0.8365 (tt0) cc_final: 0.7977 (tt0) REVERT: H 49 MET cc_start: 0.8893 (mmm) cc_final: 0.8360 (mpp) REVERT: H 82 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7144 (mp10) REVERT: B 250 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (m-80) REVERT: B 356 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8665 (mp0) REVERT: B 479 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8905 (p) REVERT: B 551 MET cc_start: 0.9042 (ptm) cc_final: 0.8665 (ptt) REVERT: M 4 MET cc_start: 0.7432 (mmm) cc_final: 0.7005 (mmm) REVERT: M 39 LYS cc_start: 0.9113 (mttt) cc_final: 0.8850 (mmmm) REVERT: M 83 LEU cc_start: 0.8658 (mt) cc_final: 0.8370 (mm) REVERT: I 5 GLN cc_start: 0.9144 (tp40) cc_final: 0.8809 (mm110) REVERT: I 27 ASP cc_start: 0.7356 (t0) cc_final: 0.6962 (t0) REVERT: I 47 GLU cc_start: 0.8410 (tt0) cc_final: 0.8002 (tt0) REVERT: I 49 MET cc_start: 0.8897 (mmm) cc_final: 0.8366 (mpp) REVERT: I 82 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7095 (mp10) outliers start: 34 outliers final: 26 residues processed: 160 average time/residue: 0.2268 time to fit residues: 55.1154 Evaluate side-chains 169 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 131 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4626 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= 0.181 Angle : 0.583 9.411 17592 Z= 0.284 Chirality : 0.039 0.167 2032 Planarity : 0.004 0.040 2188 Dihedral : 3.991 35.696 1752 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.83 % Allowed : 19.57 % Favored : 77.60 % 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: 1.78 (0.22), residues: 1618 helix: 2.93 (0.18), residues: 816 sheet: -0.54 (0.34), residues: 206 loop : -0.72 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.003 0.001 HIS B 171 PHE 0.018 0.001 PHE B 231 TYR 0.017 0.001 TYR H 33 ARG 0.002 0.000 ARG M 18 *********************** 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 179 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7659 (m-80) REVERT: A 328 SER cc_start: 0.9436 (OUTLIER) cc_final: 0.9165 (p) REVERT: A 359 ASP cc_start: 0.8898 (t0) cc_final: 0.8556 (m-30) REVERT: A 479 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8919 (p) REVERT: A 551 MET cc_start: 0.9028 (ptm) cc_final: 0.8655 (ptt) REVERT: L 4 MET cc_start: 0.7223 (mmm) cc_final: 0.6670 (mmm) REVERT: L 9 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7744 (tptp) REVERT: L 11 MET cc_start: 0.8218 (mtt) cc_final: 0.7968 (mpp) REVERT: L 39 LYS cc_start: 0.9081 (mttt) cc_final: 0.8881 (mmmm) REVERT: L 89 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: H 5 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8728 (mp10) REVERT: H 27 ASP cc_start: 0.6858 (t0) cc_final: 0.6455 (t0) REVERT: H 47 GLU cc_start: 0.8379 (tt0) cc_final: 0.7973 (tt0) REVERT: H 49 MET cc_start: 0.8815 (mmm) cc_final: 0.8333 (mpp) REVERT: H 82 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7300 (mp10) REVERT: B 250 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: B 356 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8608 (mt-10) REVERT: B 418 THR cc_start: 0.8488 (m) cc_final: 0.8228 (m) REVERT: B 479 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8915 (p) REVERT: B 551 MET cc_start: 0.9003 (ptm) cc_final: 0.8625 (ptt) REVERT: M 4 MET cc_start: 0.7770 (mmm) cc_final: 0.7231 (mmm) REVERT: M 39 LYS cc_start: 0.9107 (mttt) cc_final: 0.8850 (mmmm) REVERT: M 83 LEU cc_start: 0.8653 (mt) cc_final: 0.8365 (mm) REVERT: I 5 GLN cc_start: 0.9164 (tp40) cc_final: 0.8829 (mm110) REVERT: I 27 ASP cc_start: 0.7762 (t0) cc_final: 0.7429 (t0) REVERT: I 47 GLU cc_start: 0.8404 (tt0) cc_final: 0.7977 (tt0) REVERT: I 49 MET cc_start: 0.8811 (mmm) cc_final: 0.8438 (mpp) REVERT: I 82 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7252 (mp10) outliers start: 38 outliers final: 24 residues processed: 166 average time/residue: 0.2234 time to fit residues: 55.4861 Evaluate side-chains 168 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 128 optimal weight: 0.2980 chunk 13 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12906 Z= 0.238 Angle : 0.591 8.548 17592 Z= 0.291 Chirality : 0.039 0.165 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.097 32.232 1752 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.68 % Allowed : 19.12 % Favored : 78.20 % 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: 1.69 (0.22), residues: 1618 helix: 2.79 (0.18), residues: 828 sheet: -0.64 (0.34), residues: 210 loop : -0.71 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 411 HIS 0.003 0.001 HIS A 171 PHE 0.015 0.001 PHE A 213 TYR 0.019 0.001 TYR I 33 ARG 0.001 0.000 ARG I 98 ********************** 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 170 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: A 328 SER cc_start: 0.9492 (OUTLIER) cc_final: 0.9205 (p) REVERT: A 359 ASP cc_start: 0.8908 (t0) cc_final: 0.8637 (m-30) REVERT: A 479 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 551 MET cc_start: 0.9059 (ptm) cc_final: 0.8664 (ptt) REVERT: L 4 MET cc_start: 0.7168 (mmm) cc_final: 0.6785 (mmm) REVERT: L 39 LYS cc_start: 0.9083 (mttt) cc_final: 0.8834 (mtpp) REVERT: H 5 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8717 (mp10) REVERT: H 27 ASP cc_start: 0.7167 (t0) cc_final: 0.6807 (t0) REVERT: H 47 GLU cc_start: 0.8360 (tt0) cc_final: 0.7931 (tt0) REVERT: H 49 MET cc_start: 0.8875 (mmm) cc_final: 0.8357 (mpp) REVERT: H 82 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7348 (mp10) REVERT: B 250 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: B 356 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8603 (mt-10) REVERT: B 479 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8929 (p) REVERT: B 551 MET cc_start: 0.9055 (ptm) cc_final: 0.8663 (ptt) REVERT: B 576 MET cc_start: 0.6892 (tpp) cc_final: 0.6595 (mmp) REVERT: M 4 MET cc_start: 0.7561 (mmm) cc_final: 0.7071 (mmm) REVERT: M 9 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7952 (tptp) REVERT: M 39 LYS cc_start: 0.9071 (mttt) cc_final: 0.8816 (mmmm) REVERT: M 83 LEU cc_start: 0.8691 (mt) cc_final: 0.8437 (mm) REVERT: I 5 GLN cc_start: 0.9170 (tp40) cc_final: 0.8844 (mm110) REVERT: I 27 ASP cc_start: 0.8043 (t0) cc_final: 0.7740 (t0) REVERT: I 47 GLU cc_start: 0.8423 (tt0) cc_final: 0.7944 (tt0) REVERT: I 49 MET cc_start: 0.8880 (mmm) cc_final: 0.8465 (mpp) REVERT: I 82 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7358 (mp10) outliers start: 36 outliers final: 27 residues processed: 160 average time/residue: 0.2363 time to fit residues: 56.2048 Evaluate side-chains 165 residues out of total 1378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 328 SER Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 642 HIS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 525 ILE Chi-restraints excluded: chain B residue 642 HIS Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 17 ASP Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain M residue 49 TYR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.0570 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 16 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.4160 ------------------------------------------------------------------------------- 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** ** H 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 = 0.2990 r_free = 0.2990 target = 0.053617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.045274 restraints weight = 61295.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.046783 restraints weight = 28694.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.047852 restraints weight = 17318.000| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12906 Z= 0.207 Angle : 0.586 9.419 17592 Z= 0.287 Chirality : 0.039 0.169 2032 Planarity : 0.004 0.040 2188 Dihedral : 4.036 31.753 1752 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.46 % Allowed : 19.49 % Favored : 78.05 % 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: 1.68 (0.22), residues: 1618 helix: 2.78 (0.18), residues: 828 sheet: -0.61 (0.34), residues: 206 loop : -0.72 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.003 0.001 HIS A 171 PHE 0.014 0.001 PHE B 52 TYR 0.018 0.001 TYR I 33 ARG 0.001 0.000 ARG I 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.01 seconds wall clock time: 43 minutes 24.90 seconds (2604.90 seconds total)