Starting phenix.real_space_refine on Wed Feb 4 08:08:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9npt_49632/02_2026/9npt_49632.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.014 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 36 5.16 5 C 5904 2.51 5 N 1584 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9372 Number of models: 1 Model: "" Number of chains: 15 Chain: "G" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1058 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "A" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 854 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "C" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "D" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 854 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1112 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "F" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 854 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 2 Chain: "H" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1058 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "I" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1058 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.01, per 1000 atoms: 0.21 Number of scatterers: 9372 At special positions: 0 Unit cell: (102.699, 102.699, 97.3866, 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 36 16.00 O 1848 8.00 N 1584 7.00 C 5904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 101 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS B 512 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 557 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 119 " distance=2.03 Simple disulfide: pdb=" SG CYS F 512 " - pdb=" SG CYS F 557 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 101 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG R 1 " - " ASN E 94 " " NAG S 1 " - " ASN C 94 " " NAG T 1 " - " ASN A 94 " " NAG X 1 " - " ASN F 564 " " NAG Y 1 " - " ASN D 564 " " NAG Z 1 " - " ASN B 564 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 219.3 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 20.6% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.675A pdb=" N THR G 96 " --> pdb=" O PRO G 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 55 through 58 removed outlier: 3.783A pdb=" N LYS A 58 " --> pdb=" O SER A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'B' and resid 524 through 529 removed outlier: 4.045A pdb=" N ALA B 527 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 528 " --> pdb=" O ASP B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.598A pdb=" N ARG B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 568 " --> pdb=" O ASN B 564 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER B 569 " --> pdb=" O GLN B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'C' and resid 43 through 45 No H-bonds generated for 'chain 'C' and resid 43 through 45' Processing helix chain 'C' and resid 55 through 58 removed outlier: 3.677A pdb=" N LYS C 58 " --> pdb=" O SER C 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 58' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 171 through 179 removed outlier: 3.680A pdb=" N MET C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 577 removed outlier: 3.575A pdb=" N ARG D 558 " --> pdb=" O ASN D 554 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA D 567 " --> pdb=" O ALA D 563 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER D 569 " --> pdb=" O GLN D 565 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 572 " --> pdb=" O LYS D 568 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 598 Processing helix chain 'E' and resid 43 through 45 No H-bonds generated for 'chain 'E' and resid 43 through 45' Processing helix chain 'E' and resid 55 through 58 removed outlier: 3.692A pdb=" N LYS E 58 " --> pdb=" O SER E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 533 through 537 removed outlier: 3.507A pdb=" N GLY F 537 " --> pdb=" O PRO F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 554 through 577 removed outlier: 3.692A pdb=" N LEU F 562 " --> pdb=" O ARG F 558 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS F 568 " --> pdb=" O ASN F 564 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER F 569 " --> pdb=" O GLN F 565 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU F 572 " --> pdb=" O LYS F 568 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 573 " --> pdb=" O SER F 569 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR F 577 " --> pdb=" O LEU F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 585 through 598 removed outlier: 3.541A pdb=" N TRP F 598 " --> pdb=" O LEU F 594 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.769A pdb=" N LEU H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.823A pdb=" N ARG H 70 " --> pdb=" O ASP H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 92 through 96 removed outlier: 3.725A pdb=" N THR H 96 " --> pdb=" O PRO H 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.827A pdb=" N LEU I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 70 removed outlier: 3.812A pdb=" N ARG I 70 " --> pdb=" O ASP I 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 67 through 70' Processing helix chain 'I' and resid 92 through 96 removed outlier: 3.716A pdb=" N THR I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.779A pdb=" N ARG G 38 " --> pdb=" O PHE G 47 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N PHE G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLN A 126 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N TYR G 65 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 12.935A pdb=" N HIS A 124 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS A 90 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N HIS A 123 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS A 92 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE A 125 " --> pdb=" O CYS A 92 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ASN A 94 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY A 127 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER A 96 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.864A pdb=" N LEU B 516 " --> pdb=" O ILE B 549 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A 86 " --> pdb=" O TRP B 519 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N GLY A 51 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 73 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 476 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 82 removed outlier: 8.007A pdb=" N GLU C 85 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU C 49 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N GLU C 87 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY C 51 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY C 86 " --> pdb=" O TRP D 519 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 516 " --> pdb=" O ILE D 549 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.526A pdb=" N TYR C 93 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU C 162 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N THR C 91 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 13.418A pdb=" N ASN C 164 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 11.630A pdb=" N ALA C 89 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 90 " --> pdb=" O CYS C 119 " (cutoff:3.500A) removed outlier: 12.934A pdb=" N HIS C 124 " --> pdb=" O TYR H 65 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N TYR H 65 " --> pdb=" O HIS C 124 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLN C 126 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG H 38 " --> pdb=" O PHE H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AB1, first strand: chain 'D' and resid 474 through 476 Processing sheet with id=AB2, first strand: chain 'F' and resid 544 through 549 removed outlier: 4.158A pdb=" N LEU F 516 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY E 86 " --> pdb=" O TRP F 519 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLU E 85 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU E 49 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU E 87 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY E 51 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 73 Processing sheet with id=AB4, first strand: chain 'E' and resid 89 through 98 removed outlier: 6.527A pdb=" N LYS E 90 " --> pdb=" O THR E 121 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N HIS E 123 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N CYS E 92 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE E 125 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN E 94 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLY E 127 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER E 96 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 12.858A pdb=" N HIS E 124 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 10.148A pdb=" N TYR I 65 " --> pdb=" O HIS E 124 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N GLN E 126 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR I 63 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N PHE I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG I 38 " --> pdb=" O PHE I 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'I' and resid 4 through 7 316 hydrogen bonds defined for protein. 804 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: 1.34 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2209 1.33 - 1.45: 2181 1.45 - 1.57: 5129 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 9573 Sorted by residual: bond pdb=" N TYR G 114 " pdb=" CA TYR G 114 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.17e-02 7.31e+03 8.71e+00 bond pdb=" N SER G 111 " pdb=" CA SER G 111 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.80e+00 bond pdb=" N LEU G 112 " pdb=" CA LEU G 112 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.60e+00 bond pdb=" N GLY I 115 " pdb=" CA GLY I 115 " ideal model delta sigma weight residual 1.446 1.474 -0.028 1.11e-02 8.12e+03 6.25e+00 bond pdb=" N GLY H 115 " pdb=" CA GLY H 115 " ideal model delta sigma weight residual 1.446 1.474 -0.027 1.11e-02 8.12e+03 6.05e+00 ... (remaining 9568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 12320 2.09 - 4.18: 518 4.18 - 6.27: 98 6.27 - 8.36: 29 8.36 - 10.45: 10 Bond angle restraints: 12975 Sorted by residual: angle pdb=" C SER I 111 " pdb=" N LEU I 112 " pdb=" CA LEU I 112 " ideal model delta sigma weight residual 121.56 129.80 -8.24 1.56e+00 4.11e-01 2.79e+01 angle pdb=" N PHE A 179 " pdb=" CA PHE A 179 " pdb=" C PHE A 179 " ideal model delta sigma weight residual 111.02 116.79 -5.77 1.22e+00 6.72e-01 2.23e+01 angle pdb=" C PHE G 58 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " ideal model delta sigma weight residual 121.97 129.49 -7.52 1.80e+00 3.09e-01 1.74e+01 angle pdb=" C TRP I 107 " pdb=" N ALA I 108 " pdb=" CA ALA I 108 " ideal model delta sigma weight residual 123.47 129.64 -6.17 1.53e+00 4.27e-01 1.63e+01 angle pdb=" CB ARG H 53 " pdb=" CG ARG H 53 " pdb=" CD ARG H 53 " ideal model delta sigma weight residual 111.30 120.52 -9.22 2.30e+00 1.89e-01 1.61e+01 ... (remaining 12970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 5575 24.16 - 48.31: 248 48.31 - 72.47: 63 72.47 - 96.63: 28 96.63 - 120.79: 44 Dihedral angle restraints: 5958 sinusoidal: 2637 harmonic: 3321 Sorted by residual: dihedral pdb=" CA SER B 473 " pdb=" C SER B 473 " pdb=" N PHE B 474 " pdb=" CA PHE B 474 " ideal model delta harmonic sigma weight residual 180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual -180.00 -158.83 -21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE C 178 " pdb=" C ILE C 178 " pdb=" N PHE C 179 " pdb=" CA PHE C 179 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1252 0.072 - 0.144: 210 0.144 - 0.215: 25 0.215 - 0.287: 7 0.287 - 0.359: 3 Chirality restraints: 1497 Sorted by residual: chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.51e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.29e+02 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.38e+01 ... (remaining 1494 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 109 " -0.051 5.00e-02 4.00e+02 7.73e-02 9.57e+00 pdb=" N PRO E 110 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 110 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 110 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 76 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO E 77 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 77 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 77 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 109 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO A 110 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 110 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 110 " -0.042 5.00e-02 4.00e+02 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1319 2.77 - 3.30: 8035 3.30 - 3.83: 14936 3.83 - 4.37: 17191 4.37 - 4.90: 30735 Nonbonded interactions: 72216 Sorted by model distance: nonbonded pdb=" OD1 ASP F 525 " pdb=" OG SER F 531 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASN C 129 " pdb=" OH TYR H 55 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR G 55 " pdb=" OD1 ASN A 129 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR E 83 " pdb=" O TYR E 146 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR B 582 " pdb=" OE2 GLU F 579 " model vdw 2.302 3.040 ... (remaining 72211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.005 0.048 9606 Z= 0.273 Angle : 1.058 10.890 13065 Z= 0.532 Chirality : 0.058 0.359 1497 Planarity : 0.008 0.077 1626 Dihedral : 18.998 120.785 3795 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.46 % Favored : 94.56 % Rotamer: Outliers : 0.62 % Allowed : 0.31 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.22), residues: 1122 helix: -2.10 (0.33), residues: 160 sheet: -0.19 (0.26), residues: 340 loop : -1.82 (0.21), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 156 TYR 0.020 0.001 TYR H 124 PHE 0.030 0.003 PHE I 54 TRP 0.043 0.003 TRP C 70 HIS 0.006 0.001 HIS E 175 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9573) covalent geometry : angle 1.02084 (12975) SS BOND : bond 0.00237 ( 9) SS BOND : angle 0.93453 ( 18) hydrogen bonds : bond 0.16597 ( 308) hydrogen bonds : angle 6.69825 ( 804) link_ALPHA1-3 : bond 0.04493 ( 3) link_ALPHA1-3 : angle 2.76730 ( 9) link_ALPHA1-6 : bond 0.03403 ( 3) link_ALPHA1-6 : angle 4.99946 ( 9) link_BETA1-4 : bond 0.03201 ( 12) link_BETA1-4 : angle 3.65776 ( 36) link_NAG-ASN : bond 0.01139 ( 6) link_NAG-ASN : angle 4.15737 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 391 time to evaluate : 0.468 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: symmetry clash REVERT: D 555 LEU cc_start: 0.8557 (tp) cc_final: 0.8009 (tp) REVERT: H 89 ASN cc_start: 0.8634 (m-40) cc_final: 0.8394 (m110) outliers start: 6 outliers final: 4 residues processed: 392 average time/residue: 0.5342 time to fit residues: 221.9116 Evaluate side-chains 234 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain H residue 114 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 ASN G 89 ASN G 113 GLN ** A 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS E 80 ASN E 128 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN I 89 ASN I 119 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.102771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071198 restraints weight = 18606.157| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.82 r_work: 0.2858 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9606 Z= 0.172 Angle : 0.792 8.417 13065 Z= 0.383 Chirality : 0.047 0.319 1497 Planarity : 0.006 0.053 1626 Dihedral : 14.542 108.869 1739 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.19 % Favored : 95.28 % Rotamer: Outliers : 4.73 % Allowed : 18.52 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.23), residues: 1122 helix: -0.73 (0.40), residues: 160 sheet: -0.12 (0.29), residues: 293 loop : -1.65 (0.21), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 176 TYR 0.023 0.002 TYR H 124 PHE 0.024 0.002 PHE I 54 TRP 0.018 0.002 TRP C 70 HIS 0.004 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9573) covalent geometry : angle 0.76469 (12975) SS BOND : bond 0.00237 ( 9) SS BOND : angle 1.15716 ( 18) hydrogen bonds : bond 0.04349 ( 308) hydrogen bonds : angle 5.10955 ( 804) link_ALPHA1-3 : bond 0.00488 ( 3) link_ALPHA1-3 : angle 2.28106 ( 9) link_ALPHA1-6 : bond 0.00787 ( 3) link_ALPHA1-6 : angle 2.12672 ( 9) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 2.62518 ( 36) link_NAG-ASN : bond 0.00947 ( 6) link_NAG-ASN : angle 3.72328 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 70 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8311 (mmm-85) REVERT: G 78 ASP cc_start: 0.8172 (t0) cc_final: 0.7136 (t0) REVERT: G 111 SER cc_start: 0.7896 (t) cc_final: 0.7557 (m) REVERT: G 113 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: G 135 VAL cc_start: 0.8001 (t) cc_final: 0.7600 (p) REVERT: B 578 THR cc_start: 0.8071 (p) cc_final: 0.7590 (t) REVERT: B 581 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6812 (ptm160) REVERT: B 592 ASP cc_start: 0.8654 (m-30) cc_final: 0.8430 (m-30) REVERT: C 45 GLU cc_start: 0.9093 (pm20) cc_final: 0.8668 (pp20) REVERT: C 131 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.6904 (p90) REVERT: D 579 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7456 (tp30) REVERT: E 43 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8607 (mtmm) REVERT: F 521 VAL cc_start: 0.8179 (OUTLIER) cc_final: 0.7963 (t) REVERT: F 597 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7428 (tmm160) REVERT: H 3 GLN cc_start: 0.7295 (mp10) cc_final: 0.5818 (pm20) REVERT: H 46 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8588 (pm20) REVERT: H 56 ASN cc_start: 0.8770 (t0) cc_final: 0.8530 (t0) REVERT: H 72 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7432 (mtp-110) REVERT: H 78 ASP cc_start: 0.8106 (t0) cc_final: 0.7324 (t0) REVERT: H 90 ASN cc_start: 0.8746 (p0) cc_final: 0.8437 (p0) REVERT: H 110 GLU cc_start: 0.8063 (pp20) cc_final: 0.7792 (pm20) REVERT: I 23 THR cc_start: 0.6470 (OUTLIER) cc_final: 0.6244 (m) REVERT: I 26 ARG cc_start: 0.9148 (ptp-110) cc_final: 0.8825 (ptp90) REVERT: I 31 LEU cc_start: 0.9009 (mp) cc_final: 0.8723 (pt) REVERT: I 46 GLU cc_start: 0.8720 (pt0) cc_final: 0.8379 (pm20) REVERT: I 72 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7471 (mtm-85) REVERT: I 78 ASP cc_start: 0.8095 (t0) cc_final: 0.7390 (t0) REVERT: I 135 VAL cc_start: 0.8023 (t) cc_final: 0.7817 (t) outliers start: 46 outliers final: 19 residues processed: 278 average time/residue: 0.5273 time to fit residues: 155.6994 Evaluate side-chains 254 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 511 ASP Chi-restraints excluded: chain D residue 550 LYS Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 101 CYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain I residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 0.0970 chunk 85 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 62 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 48 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 ASN I 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.102224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.070254 restraints weight = 18149.428| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.81 r_work: 0.2831 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9606 Z= 0.153 Angle : 0.722 8.315 13065 Z= 0.354 Chirality : 0.044 0.195 1497 Planarity : 0.004 0.047 1626 Dihedral : 10.417 104.177 1739 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.92 % Favored : 95.45 % Rotamer: Outliers : 4.63 % Allowed : 20.99 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.23), residues: 1122 helix: -0.46 (0.39), residues: 171 sheet: -0.11 (0.29), residues: 300 loop : -1.47 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 176 TYR 0.015 0.001 TYR H 32 PHE 0.019 0.001 PHE I 54 TRP 0.011 0.001 TRP I 107 HIS 0.003 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9573) covalent geometry : angle 0.69659 (12975) SS BOND : bond 0.00205 ( 9) SS BOND : angle 1.02080 ( 18) hydrogen bonds : bond 0.03826 ( 308) hydrogen bonds : angle 4.93482 ( 804) link_ALPHA1-3 : bond 0.00667 ( 3) link_ALPHA1-3 : angle 1.90356 ( 9) link_ALPHA1-6 : bond 0.00900 ( 3) link_ALPHA1-6 : angle 2.09952 ( 9) link_BETA1-4 : bond 0.00349 ( 12) link_BETA1-4 : angle 2.34170 ( 36) link_NAG-ASN : bond 0.00858 ( 6) link_NAG-ASN : angle 3.55176 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 46 GLU cc_start: 0.8480 (pt0) cc_final: 0.8188 (pm20) REVERT: G 70 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8359 (mmm-85) REVERT: G 78 ASP cc_start: 0.8230 (t0) cc_final: 0.7513 (t0) REVERT: G 111 SER cc_start: 0.8478 (t) cc_final: 0.7919 (m) REVERT: B 511 ASP cc_start: 0.6948 (t0) cc_final: 0.6652 (t0) REVERT: B 580 GLU cc_start: 0.8351 (mp0) cc_final: 0.8011 (mp0) REVERT: B 592 ASP cc_start: 0.8594 (m-30) cc_final: 0.8360 (m-30) REVERT: C 45 GLU cc_start: 0.9052 (pm20) cc_final: 0.8567 (pp20) REVERT: C 131 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7178 (p90) REVERT: E 43 LYS cc_start: 0.8800 (mtpt) cc_final: 0.8579 (mtmm) REVERT: E 45 GLU cc_start: 0.8501 (pp20) cc_final: 0.8286 (pp20) REVERT: F 597 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7442 (tmm-80) REVERT: H 46 GLU cc_start: 0.8820 (pt0) cc_final: 0.8590 (pm20) REVERT: H 56 ASN cc_start: 0.8900 (t0) cc_final: 0.8254 (t0) REVERT: H 72 ARG cc_start: 0.7813 (mtm110) cc_final: 0.7306 (mtp-110) REVERT: H 78 ASP cc_start: 0.8238 (t0) cc_final: 0.7931 (t0) REVERT: I 26 ARG cc_start: 0.9143 (ptp-110) cc_final: 0.8820 (ptt90) REVERT: I 31 LEU cc_start: 0.9046 (mp) cc_final: 0.8344 (pt) REVERT: I 46 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: I 53 ARG cc_start: 0.8319 (tmm-80) cc_final: 0.7525 (ttm-80) REVERT: I 72 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7434 (mtm-85) REVERT: I 78 ASP cc_start: 0.8170 (t0) cc_final: 0.7541 (t0) REVERT: I 111 SER cc_start: 0.8057 (t) cc_final: 0.7455 (m) outliers start: 45 outliers final: 15 residues processed: 254 average time/residue: 0.5664 time to fit residues: 152.6693 Evaluate side-chains 235 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 113 GLN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 48 HIS A 164 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 126 GLN E 128 GLN H 56 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.073830 restraints weight = 18646.784| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.32 r_work: 0.2947 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9606 Z= 0.161 Angle : 0.696 8.727 13065 Z= 0.343 Chirality : 0.043 0.177 1497 Planarity : 0.004 0.042 1626 Dihedral : 9.050 101.942 1739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 4.19 % Favored : 95.19 % Rotamer: Outliers : 4.32 % Allowed : 20.78 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.23), residues: 1122 helix: -0.23 (0.40), residues: 171 sheet: -0.07 (0.28), residues: 318 loop : -1.39 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 176 TYR 0.010 0.001 TYR F 544 PHE 0.018 0.001 PHE B 474 TRP 0.010 0.001 TRP D 519 HIS 0.004 0.001 HIS A 48 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 9573) covalent geometry : angle 0.67582 (12975) SS BOND : bond 0.00183 ( 9) SS BOND : angle 0.80595 ( 18) hydrogen bonds : bond 0.03690 ( 308) hydrogen bonds : angle 4.86043 ( 804) link_ALPHA1-3 : bond 0.00697 ( 3) link_ALPHA1-3 : angle 1.53290 ( 9) link_ALPHA1-6 : bond 0.00934 ( 3) link_ALPHA1-6 : angle 2.13086 ( 9) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 2.11684 ( 36) link_NAG-ASN : bond 0.00847 ( 6) link_NAG-ASN : angle 3.11613 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 229 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 GLN cc_start: 0.8451 (tp40) cc_final: 0.7854 (pp30) REVERT: G 46 GLU cc_start: 0.8801 (pt0) cc_final: 0.8575 (pm20) REVERT: G 70 ARG cc_start: 0.8778 (tpp80) cc_final: 0.8397 (mmm-85) REVERT: G 78 ASP cc_start: 0.8732 (t0) cc_final: 0.8179 (t0) REVERT: G 92 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8664 (mmmt) REVERT: A 90 LYS cc_start: 0.8821 (mtpm) cc_final: 0.8524 (mtmt) REVERT: A 108 ASP cc_start: 0.8942 (m-30) cc_final: 0.8725 (m-30) REVERT: B 488 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5939 (pp) REVERT: B 511 ASP cc_start: 0.6941 (t0) cc_final: 0.6675 (t0) REVERT: B 581 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7475 (mtp180) REVERT: B 592 ASP cc_start: 0.8853 (m-30) cc_final: 0.8641 (m-30) REVERT: C 131 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7615 (p90) REVERT: E 43 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8897 (mtmm) REVERT: E 112 ASN cc_start: 0.8874 (p0) cc_final: 0.8643 (p0) REVERT: E 131 HIS cc_start: 0.8476 (OUTLIER) cc_final: 0.7539 (p90) REVERT: F 597 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7516 (ttt180) REVERT: H 18 LEU cc_start: 0.8572 (tp) cc_final: 0.8355 (tp) REVERT: H 46 GLU cc_start: 0.8908 (pt0) cc_final: 0.8703 (pp20) REVERT: H 56 ASN cc_start: 0.8906 (t0) cc_final: 0.8539 (t0) REVERT: H 72 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7933 (mtp-110) REVERT: H 78 ASP cc_start: 0.8741 (t0) cc_final: 0.8351 (t0) REVERT: I 3 GLN cc_start: 0.7652 (pm20) cc_final: 0.7355 (pm20) REVERT: I 26 ARG cc_start: 0.8790 (ptp-110) cc_final: 0.8570 (ptp90) REVERT: I 31 LEU cc_start: 0.9171 (mp) cc_final: 0.8407 (pt) REVERT: I 53 ARG cc_start: 0.8509 (tmm-80) cc_final: 0.7797 (ttm-80) REVERT: I 78 ASP cc_start: 0.8739 (t0) cc_final: 0.8080 (t0) REVERT: I 111 SER cc_start: 0.7994 (t) cc_final: 0.7592 (m) outliers start: 42 outliers final: 18 residues processed: 253 average time/residue: 0.5651 time to fit residues: 151.4208 Evaluate side-chains 237 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 116 ASN Chi-restraints excluded: chain I residue 123 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 57 GLN A 164 ASN A 175 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN I 119 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069858 restraints weight = 18658.378| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.52 r_work: 0.2833 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9606 Z= 0.203 Angle : 0.699 9.093 13065 Z= 0.349 Chirality : 0.044 0.190 1497 Planarity : 0.004 0.039 1626 Dihedral : 8.565 102.324 1739 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 4.73 % Allowed : 20.78 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.23), residues: 1122 helix: -0.06 (0.41), residues: 171 sheet: 0.09 (0.28), residues: 318 loop : -1.58 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 176 TYR 0.013 0.001 TYR F 544 PHE 0.014 0.002 PHE B 474 TRP 0.009 0.001 TRP B 519 HIS 0.004 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9573) covalent geometry : angle 0.68324 (12975) SS BOND : bond 0.00272 ( 9) SS BOND : angle 1.04530 ( 18) hydrogen bonds : bond 0.03967 ( 308) hydrogen bonds : angle 4.80435 ( 804) link_ALPHA1-3 : bond 0.00638 ( 3) link_ALPHA1-3 : angle 1.48460 ( 9) link_ALPHA1-6 : bond 0.00963 ( 3) link_ALPHA1-6 : angle 2.23589 ( 9) link_BETA1-4 : bond 0.00425 ( 12) link_BETA1-4 : angle 1.98833 ( 36) link_NAG-ASN : bond 0.00449 ( 6) link_NAG-ASN : angle 2.40196 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 GLN cc_start: 0.8332 (tp40) cc_final: 0.7714 (pp30) REVERT: G 46 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8292 (pm20) REVERT: G 70 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8368 (mmm-85) REVERT: G 78 ASP cc_start: 0.8603 (t0) cc_final: 0.8031 (t0) REVERT: G 107 TRP cc_start: 0.7008 (OUTLIER) cc_final: 0.6476 (p90) REVERT: G 114 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8430 (p90) REVERT: B 511 ASP cc_start: 0.7233 (t0) cc_final: 0.7024 (t0) REVERT: B 579 GLU cc_start: 0.7612 (tp30) cc_final: 0.7294 (tt0) REVERT: B 580 GLU cc_start: 0.8367 (mp0) cc_final: 0.7954 (mp0) REVERT: C 131 HIS cc_start: 0.8524 (OUTLIER) cc_final: 0.7742 (p90) REVERT: D 598 TRP cc_start: 0.6073 (m-10) cc_final: 0.5580 (m-10) REVERT: E 43 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8764 (mtmm) REVERT: E 45 GLU cc_start: 0.9295 (pt0) cc_final: 0.8719 (pp20) REVERT: E 112 ASN cc_start: 0.8970 (p0) cc_final: 0.8692 (p0) REVERT: E 128 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: E 131 HIS cc_start: 0.8461 (OUTLIER) cc_final: 0.7528 (p90) REVERT: F 543 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8892 (tt) REVERT: F 581 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7447 (pmt-80) REVERT: F 597 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7455 (tmm-80) REVERT: H 56 ASN cc_start: 0.9105 (t0) cc_final: 0.8594 (t0) REVERT: H 72 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7839 (mtm-85) REVERT: H 78 ASP cc_start: 0.8554 (t0) cc_final: 0.7691 (t0) REVERT: I 3 GLN cc_start: 0.7603 (pm20) cc_final: 0.7173 (pm20) REVERT: I 26 ARG cc_start: 0.9029 (ptp-110) cc_final: 0.8827 (ptp90) REVERT: I 31 LEU cc_start: 0.9200 (mp) cc_final: 0.8936 (pt) REVERT: I 46 GLU cc_start: 0.8782 (pt0) cc_final: 0.8388 (pp20) REVERT: I 56 ASN cc_start: 0.9176 (t0) cc_final: 0.8550 (t0) REVERT: I 78 ASP cc_start: 0.8531 (t0) cc_final: 0.7473 (t0) REVERT: I 111 SER cc_start: 0.8065 (t) cc_final: 0.7600 (m) outliers start: 46 outliers final: 20 residues processed: 253 average time/residue: 0.6320 time to fit residues: 169.0263 Evaluate side-chains 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 107 TRP Chi-restraints excluded: chain G residue 114 TYR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain D residue 558 ARG Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 116 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 164 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN I 89 ASN I 119 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.071455 restraints weight = 18777.042| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 3.35 r_work: 0.2886 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9606 Z= 0.174 Angle : 0.701 9.541 13065 Z= 0.349 Chirality : 0.044 0.177 1497 Planarity : 0.004 0.047 1626 Dihedral : 8.222 99.120 1739 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.28 % Favored : 95.19 % Rotamer: Outliers : 4.42 % Allowed : 21.60 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1122 helix: -0.04 (0.41), residues: 174 sheet: 0.25 (0.29), residues: 309 loop : -1.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 176 TYR 0.027 0.001 TYR G 99 PHE 0.015 0.001 PHE B 474 TRP 0.013 0.001 TRP I 107 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9573) covalent geometry : angle 0.68754 (12975) SS BOND : bond 0.00231 ( 9) SS BOND : angle 0.90594 ( 18) hydrogen bonds : bond 0.03778 ( 308) hydrogen bonds : angle 4.79078 ( 804) link_ALPHA1-3 : bond 0.00628 ( 3) link_ALPHA1-3 : angle 1.44642 ( 9) link_ALPHA1-6 : bond 0.00927 ( 3) link_ALPHA1-6 : angle 2.23928 ( 9) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 1.87768 ( 36) link_NAG-ASN : bond 0.00468 ( 6) link_NAG-ASN : angle 2.15818 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.8041 (mt0) cc_final: 0.7581 (mp10) REVERT: G 5 GLN cc_start: 0.8472 (tp40) cc_final: 0.7904 (pp30) REVERT: G 46 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: G 65 TYR cc_start: 0.8561 (m-10) cc_final: 0.8358 (m-10) REVERT: G 70 ARG cc_start: 0.8805 (tpp80) cc_final: 0.8594 (tpp-160) REVERT: G 78 ASP cc_start: 0.8771 (t0) cc_final: 0.8184 (t0) REVERT: G 114 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8472 (p90) REVERT: A 90 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8537 (mtmt) REVERT: A 128 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: B 511 ASP cc_start: 0.7228 (t0) cc_final: 0.7016 (t0) REVERT: B 579 GLU cc_start: 0.7598 (tp30) cc_final: 0.7289 (tt0) REVERT: C 131 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.7922 (p90) REVERT: E 43 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8939 (mtmm) REVERT: E 45 GLU cc_start: 0.9220 (pt0) cc_final: 0.8747 (pp20) REVERT: E 99 ASP cc_start: 0.8803 (p0) cc_final: 0.8583 (p0) REVERT: E 128 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: E 131 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7686 (p90) REVERT: F 543 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9022 (tt) REVERT: F 581 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7209 (pmt-80) REVERT: F 597 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7641 (tmm-80) REVERT: H 26 ARG cc_start: 0.8679 (ptp90) cc_final: 0.8474 (pmt170) REVERT: H 43 LYS cc_start: 0.8350 (pttm) cc_final: 0.8077 (pmtt) REVERT: H 56 ASN cc_start: 0.9056 (t0) cc_final: 0.8611 (t0) REVERT: H 72 ARG cc_start: 0.8502 (mtm110) cc_final: 0.8057 (mtm-85) REVERT: H 78 ASP cc_start: 0.8656 (t0) cc_final: 0.8364 (t0) REVERT: H 106 GLU cc_start: 0.8263 (pm20) cc_final: 0.8052 (pm20) REVERT: I 3 GLN cc_start: 0.7850 (pm20) cc_final: 0.7545 (pm20) REVERT: I 26 ARG cc_start: 0.8870 (ptp-110) cc_final: 0.8651 (ptp90) REVERT: I 31 LEU cc_start: 0.9263 (mp) cc_final: 0.9028 (pt) REVERT: I 46 GLU cc_start: 0.8836 (pt0) cc_final: 0.8524 (pp20) REVERT: I 56 ASN cc_start: 0.9094 (t0) cc_final: 0.8564 (t0) REVERT: I 78 ASP cc_start: 0.8655 (t0) cc_final: 0.8035 (t0) REVERT: I 111 SER cc_start: 0.8051 (t) cc_final: 0.7688 (m) REVERT: I 114 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8420 (p90) outliers start: 43 outliers final: 17 residues processed: 247 average time/residue: 0.6045 time to fit residues: 157.9531 Evaluate side-chains 239 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 114 TYR Chi-restraints excluded: chain G residue 116 ASN Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 114 TYR Chi-restraints excluded: chain I residue 123 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.0670 chunk 90 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 164 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN E 48 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN I 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.102408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.072664 restraints weight = 18605.075| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.33 r_work: 0.2922 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9606 Z= 0.132 Angle : 0.692 10.076 13065 Z= 0.339 Chirality : 0.043 0.173 1497 Planarity : 0.004 0.049 1626 Dihedral : 7.842 94.654 1739 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.55 % Favored : 94.92 % Rotamer: Outliers : 3.29 % Allowed : 23.66 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.23), residues: 1122 helix: 0.01 (0.41), residues: 174 sheet: 0.24 (0.29), residues: 312 loop : -1.42 (0.21), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 176 TYR 0.010 0.001 TYR E 83 PHE 0.014 0.001 PHE D 474 TRP 0.015 0.001 TRP I 107 HIS 0.002 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9573) covalent geometry : angle 0.67997 (12975) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.72280 ( 18) hydrogen bonds : bond 0.03417 ( 308) hydrogen bonds : angle 4.75797 ( 804) link_ALPHA1-3 : bond 0.00667 ( 3) link_ALPHA1-3 : angle 1.40399 ( 9) link_ALPHA1-6 : bond 0.01077 ( 3) link_ALPHA1-6 : angle 2.31917 ( 9) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 1.73941 ( 36) link_NAG-ASN : bond 0.00433 ( 6) link_NAG-ASN : angle 1.89890 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.7961 (mt0) cc_final: 0.7521 (mp10) REVERT: G 46 GLU cc_start: 0.8856 (pt0) cc_final: 0.8595 (pm20) REVERT: G 54 PHE cc_start: 0.8408 (m-80) cc_final: 0.8206 (m-80) REVERT: G 70 ARG cc_start: 0.8803 (tpp80) cc_final: 0.8383 (mmm-85) REVERT: G 78 ASP cc_start: 0.8782 (t0) cc_final: 0.8226 (t0) REVERT: A 90 LYS cc_start: 0.8837 (mtpm) cc_final: 0.8529 (mtmt) REVERT: A 128 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: A 131 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 488 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6195 (pp) REVERT: B 581 ARG cc_start: 0.7745 (mtp180) cc_final: 0.7460 (ptm160) REVERT: C 43 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8734 (mtpm) REVERT: C 45 GLU cc_start: 0.9021 (pm20) cc_final: 0.8800 (pm20) REVERT: C 131 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.7926 (p90) REVERT: D 515 GLU cc_start: 0.8946 (tt0) cc_final: 0.8660 (tp30) REVERT: E 43 LYS cc_start: 0.9175 (mtpt) cc_final: 0.8837 (mtmm) REVERT: E 45 GLU cc_start: 0.9195 (pt0) cc_final: 0.8805 (pp20) REVERT: E 99 ASP cc_start: 0.8784 (p0) cc_final: 0.8583 (p0) REVERT: E 131 HIS cc_start: 0.8544 (OUTLIER) cc_final: 0.7724 (p90) REVERT: F 543 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8966 (tt) REVERT: F 581 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7098 (pmt-80) REVERT: F 597 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7697 (tmm-80) REVERT: H 56 ASN cc_start: 0.8987 (t0) cc_final: 0.8581 (t0) REVERT: H 72 ARG cc_start: 0.8482 (mtm110) cc_final: 0.8076 (mtm-85) REVERT: H 78 ASP cc_start: 0.8728 (t0) cc_final: 0.8318 (t0) REVERT: I 3 GLN cc_start: 0.8001 (pm20) cc_final: 0.7620 (pm20) REVERT: I 31 LEU cc_start: 0.9262 (mp) cc_final: 0.9051 (pt) REVERT: I 46 GLU cc_start: 0.8874 (pt0) cc_final: 0.8577 (pp20) REVERT: I 56 ASN cc_start: 0.9004 (t0) cc_final: 0.8539 (t0) REVERT: I 78 ASP cc_start: 0.8748 (t0) cc_final: 0.8480 (t0) REVERT: I 111 SER cc_start: 0.7971 (t) cc_final: 0.7591 (m) REVERT: I 114 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.8365 (p90) outliers start: 32 outliers final: 8 residues processed: 242 average time/residue: 0.6057 time to fit residues: 155.3334 Evaluate side-chains 225 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 164 ASN C 57 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN E 48 HIS E 128 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 89 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068214 restraints weight = 18882.606| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.38 r_work: 0.2831 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9606 Z= 0.266 Angle : 0.774 10.924 13065 Z= 0.385 Chirality : 0.046 0.194 1497 Planarity : 0.005 0.054 1626 Dihedral : 7.689 88.595 1737 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.90 % Favored : 94.56 % Rotamer: Outliers : 3.81 % Allowed : 24.38 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.23), residues: 1122 helix: 0.03 (0.41), residues: 174 sheet: 0.09 (0.28), residues: 315 loop : -1.51 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 176 TYR 0.014 0.002 TYR F 544 PHE 0.013 0.002 PHE F 583 TRP 0.014 0.002 TRP F 598 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 9573) covalent geometry : angle 0.75831 (12975) SS BOND : bond 0.00375 ( 9) SS BOND : angle 1.52105 ( 18) hydrogen bonds : bond 0.04404 ( 308) hydrogen bonds : angle 4.83096 ( 804) link_ALPHA1-3 : bond 0.00446 ( 3) link_ALPHA1-3 : angle 1.60148 ( 9) link_ALPHA1-6 : bond 0.00862 ( 3) link_ALPHA1-6 : angle 2.63801 ( 9) link_BETA1-4 : bond 0.00435 ( 12) link_BETA1-4 : angle 1.97696 ( 36) link_NAG-ASN : bond 0.00411 ( 6) link_NAG-ASN : angle 2.34260 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.372 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: G 3 GLN cc_start: 0.7961 (mt0) cc_final: 0.7488 (mp10) REVERT: G 5 GLN cc_start: 0.8431 (tp40) cc_final: 0.7896 (pp30) REVERT: G 70 ARG cc_start: 0.8818 (tpp80) cc_final: 0.8339 (mmm-85) REVERT: G 78 ASP cc_start: 0.8826 (t0) cc_final: 0.8245 (t0) REVERT: A 128 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: A 131 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.7896 (p90) REVERT: B 579 GLU cc_start: 0.7677 (tp30) cc_final: 0.7335 (tt0) REVERT: C 131 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8063 (p90) REVERT: D 517 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8589 (mtt-85) REVERT: D 586 ILE cc_start: 0.9345 (pt) cc_final: 0.9064 (mp) REVERT: E 43 LYS cc_start: 0.9202 (mtpt) cc_final: 0.8950 (mtmm) REVERT: E 45 GLU cc_start: 0.9248 (pt0) cc_final: 0.8770 (pp20) REVERT: E 99 ASP cc_start: 0.8819 (p0) cc_final: 0.8593 (p0) REVERT: E 131 HIS cc_start: 0.8775 (OUTLIER) cc_final: 0.7944 (p90) REVERT: F 581 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7379 (pmt-80) REVERT: F 592 ASP cc_start: 0.9011 (m-30) cc_final: 0.8763 (m-30) REVERT: F 597 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7770 (tmm-80) REVERT: H 5 GLN cc_start: 0.7964 (mp10) cc_final: 0.7571 (pp30) REVERT: H 43 LYS cc_start: 0.8308 (pmmt) cc_final: 0.8008 (pmtt) REVERT: H 70 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8637 (tpp-160) REVERT: H 72 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8148 (mtm-85) REVERT: H 78 ASP cc_start: 0.8772 (t0) cc_final: 0.8290 (t0) REVERT: I 3 GLN cc_start: 0.7851 (pm20) cc_final: 0.7630 (pm20) REVERT: I 31 LEU cc_start: 0.9354 (mp) cc_final: 0.9086 (pt) REVERT: I 46 GLU cc_start: 0.8814 (pt0) cc_final: 0.8535 (pp20) REVERT: I 56 ASN cc_start: 0.9232 (t0) cc_final: 0.8669 (t0) REVERT: I 78 ASP cc_start: 0.8790 (t0) cc_final: 0.8510 (t70) REVERT: I 114 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.8452 (p90) REVERT: I 123 LYS cc_start: 0.8151 (mttp) cc_final: 0.7892 (pttm) outliers start: 37 outliers final: 15 residues processed: 237 average time/residue: 0.6032 time to fit residues: 151.3670 Evaluate side-chains 227 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 131 HIS Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain F residue 597 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN A 164 ASN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN I 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071369 restraints weight = 18796.648| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.52 r_work: 0.2962 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9606 Z= 0.170 Angle : 0.758 11.557 13065 Z= 0.371 Chirality : 0.044 0.174 1497 Planarity : 0.005 0.061 1626 Dihedral : 7.133 81.512 1737 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.63 % Favored : 94.92 % Rotamer: Outliers : 2.67 % Allowed : 26.75 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.23), residues: 1122 helix: 0.07 (0.41), residues: 174 sheet: 0.11 (0.29), residues: 315 loop : -1.49 (0.21), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 176 TYR 0.022 0.001 TYR H 32 PHE 0.014 0.002 PHE B 474 TRP 0.014 0.001 TRP H 107 HIS 0.003 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9573) covalent geometry : angle 0.74681 (12975) SS BOND : bond 0.00225 ( 9) SS BOND : angle 0.94543 ( 18) hydrogen bonds : bond 0.03795 ( 308) hydrogen bonds : angle 4.78167 ( 804) link_ALPHA1-3 : bond 0.00609 ( 3) link_ALPHA1-3 : angle 1.45027 ( 9) link_ALPHA1-6 : bond 0.01192 ( 3) link_ALPHA1-6 : angle 2.51106 ( 9) link_BETA1-4 : bond 0.00395 ( 12) link_BETA1-4 : angle 1.74000 ( 36) link_NAG-ASN : bond 0.00409 ( 6) link_NAG-ASN : angle 1.93328 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.7847 (mt0) cc_final: 0.7375 (mp10) REVERT: G 5 GLN cc_start: 0.8382 (tp40) cc_final: 0.7894 (pp30) REVERT: G 31 LEU cc_start: 0.9416 (mp) cc_final: 0.9001 (mt) REVERT: G 32 TYR cc_start: 0.8950 (m-80) cc_final: 0.8624 (m-80) REVERT: G 46 GLU cc_start: 0.8774 (pt0) cc_final: 0.8469 (pm20) REVERT: G 53 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7574 (ttm-80) REVERT: G 54 PHE cc_start: 0.8502 (m-80) cc_final: 0.8265 (m-80) REVERT: G 70 ARG cc_start: 0.8830 (tpp80) cc_final: 0.8342 (mmm-85) REVERT: G 78 ASP cc_start: 0.8819 (t0) cc_final: 0.7833 (t0) REVERT: A 90 LYS cc_start: 0.8928 (mtpm) cc_final: 0.8617 (mtmt) REVERT: A 128 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: A 131 HIS cc_start: 0.8766 (OUTLIER) cc_final: 0.7890 (p90) REVERT: B 579 GLU cc_start: 0.7705 (tp30) cc_final: 0.7302 (tt0) REVERT: C 43 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8724 (mtpm) REVERT: C 45 GLU cc_start: 0.9119 (pm20) cc_final: 0.8862 (pm20) REVERT: D 517 ARG cc_start: 0.8849 (mtp85) cc_final: 0.8567 (mtt-85) REVERT: D 586 ILE cc_start: 0.9286 (pt) cc_final: 0.9002 (mp) REVERT: D 592 ASP cc_start: 0.8963 (m-30) cc_final: 0.8752 (m-30) REVERT: E 45 GLU cc_start: 0.9200 (pt0) cc_final: 0.8851 (pp20) REVERT: E 99 ASP cc_start: 0.8798 (p0) cc_final: 0.8596 (p0) REVERT: E 131 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.7938 (p90) REVERT: F 581 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7536 (pmt-80) REVERT: F 592 ASP cc_start: 0.9046 (m-30) cc_final: 0.8804 (m-30) REVERT: H 5 GLN cc_start: 0.7980 (mp10) cc_final: 0.7582 (pp30) REVERT: H 43 LYS cc_start: 0.8298 (pmmt) cc_final: 0.7948 (pmtt) REVERT: H 56 ASN cc_start: 0.9142 (t0) cc_final: 0.8657 (t0) REVERT: H 70 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8626 (tpp-160) REVERT: H 72 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8235 (mtm-85) REVERT: H 78 ASP cc_start: 0.8704 (t0) cc_final: 0.8260 (t0) REVERT: H 127 TRP cc_start: 0.8243 (m100) cc_final: 0.7945 (m100) REVERT: I 31 LEU cc_start: 0.9334 (mp) cc_final: 0.9021 (pt) REVERT: I 46 GLU cc_start: 0.8769 (pt0) cc_final: 0.8471 (pp20) REVERT: I 56 ASN cc_start: 0.9209 (t0) cc_final: 0.8661 (t0) REVERT: I 70 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8402 (tpp-160) REVERT: I 78 ASP cc_start: 0.8885 (t0) cc_final: 0.8539 (t70) REVERT: I 111 SER cc_start: 0.8018 (t) cc_final: 0.7579 (m) REVERT: I 114 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8411 (p90) outliers start: 26 outliers final: 12 residues processed: 232 average time/residue: 0.5543 time to fit residues: 135.9659 Evaluate side-chains 227 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 94 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN I 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.102515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.071740 restraints weight = 18788.422| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.55 r_work: 0.2992 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9606 Z= 0.156 Angle : 0.752 10.864 13065 Z= 0.370 Chirality : 0.044 0.176 1497 Planarity : 0.005 0.065 1626 Dihedral : 6.553 75.393 1735 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.63 % Favored : 94.92 % Rotamer: Outliers : 2.67 % Allowed : 27.47 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1122 helix: 0.06 (0.41), residues: 174 sheet: 0.09 (0.29), residues: 318 loop : -1.47 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 176 TYR 0.015 0.001 TYR G 32 PHE 0.013 0.001 PHE I 54 TRP 0.012 0.001 TRP I 36 HIS 0.002 0.001 HIS H 119 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9573) covalent geometry : angle 0.74200 (12975) SS BOND : bond 0.00210 ( 9) SS BOND : angle 0.97672 ( 18) hydrogen bonds : bond 0.03611 ( 308) hydrogen bonds : angle 4.78672 ( 804) link_ALPHA1-3 : bond 0.00623 ( 3) link_ALPHA1-3 : angle 1.43555 ( 9) link_ALPHA1-6 : bond 0.01295 ( 3) link_ALPHA1-6 : angle 2.26114 ( 9) link_BETA1-4 : bond 0.00404 ( 12) link_BETA1-4 : angle 1.70322 ( 36) link_NAG-ASN : bond 0.00377 ( 6) link_NAG-ASN : angle 1.81854 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 223 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.7873 (mt0) cc_final: 0.7432 (mp10) REVERT: G 5 GLN cc_start: 0.8453 (tp40) cc_final: 0.8089 (pp30) REVERT: G 31 LEU cc_start: 0.9439 (mp) cc_final: 0.9013 (mt) REVERT: G 32 TYR cc_start: 0.8980 (m-80) cc_final: 0.8718 (m-80) REVERT: G 46 GLU cc_start: 0.8819 (pt0) cc_final: 0.8557 (pm20) REVERT: G 53 ARG cc_start: 0.8329 (tmm-80) cc_final: 0.7702 (ttm-80) REVERT: G 54 PHE cc_start: 0.8520 (m-80) cc_final: 0.8285 (m-80) REVERT: G 70 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8357 (mmm-85) REVERT: G 78 ASP cc_start: 0.8684 (t0) cc_final: 0.8447 (t0) REVERT: G 114 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8495 (p90) REVERT: A 90 LYS cc_start: 0.8931 (mtpm) cc_final: 0.8654 (mtmt) REVERT: A 128 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7518 (tt0) REVERT: A 131 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.7947 (p90) REVERT: B 511 ASP cc_start: 0.8473 (p0) cc_final: 0.8032 (p0) REVERT: B 579 GLU cc_start: 0.7587 (tp30) cc_final: 0.7279 (tt0) REVERT: C 43 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8775 (mtpm) REVERT: C 45 GLU cc_start: 0.9073 (pm20) cc_final: 0.8847 (pm20) REVERT: D 517 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8545 (mtt-85) REVERT: D 586 ILE cc_start: 0.9277 (pt) cc_final: 0.9009 (mp) REVERT: E 45 GLU cc_start: 0.9139 (pt0) cc_final: 0.8867 (pp20) REVERT: E 99 ASP cc_start: 0.8775 (p0) cc_final: 0.8563 (p0) REVERT: E 131 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.7945 (p90) REVERT: F 581 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (ppt170) REVERT: F 592 ASP cc_start: 0.9023 (m-30) cc_final: 0.8789 (m-30) REVERT: H 5 GLN cc_start: 0.8004 (mp10) cc_final: 0.7501 (pp30) REVERT: H 19 ARG cc_start: 0.8980 (ttt90) cc_final: 0.8722 (ttt-90) REVERT: H 43 LYS cc_start: 0.8280 (pmmt) cc_final: 0.7937 (pmtt) REVERT: H 54 PHE cc_start: 0.8365 (m-80) cc_final: 0.8159 (m-80) REVERT: H 56 ASN cc_start: 0.9055 (t0) cc_final: 0.8692 (t0) REVERT: H 70 ARG cc_start: 0.8805 (tpp80) cc_final: 0.8600 (tpp-160) REVERT: H 72 ARG cc_start: 0.8666 (mtm110) cc_final: 0.8258 (mtm-85) REVERT: H 78 ASP cc_start: 0.8749 (t0) cc_final: 0.8334 (t0) REVERT: H 127 TRP cc_start: 0.8273 (m100) cc_final: 0.7981 (m100) REVERT: I 31 LEU cc_start: 0.9337 (mp) cc_final: 0.9054 (pt) REVERT: I 46 GLU cc_start: 0.8749 (pt0) cc_final: 0.8505 (pp20) REVERT: I 56 ASN cc_start: 0.9089 (t0) cc_final: 0.8648 (t0) REVERT: I 78 ASP cc_start: 0.8911 (t0) cc_final: 0.8626 (t70) REVERT: I 106 GLU cc_start: 0.8290 (pp20) cc_final: 0.7765 (pp20) REVERT: I 111 SER cc_start: 0.7853 (t) cc_final: 0.7533 (m) REVERT: I 114 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8518 (p90) outliers start: 26 outliers final: 13 residues processed: 235 average time/residue: 0.5757 time to fit residues: 143.3275 Evaluate side-chains 233 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 114 TYR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain D residue 578 THR Chi-restraints excluded: chain E residue 131 HIS Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 581 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 114 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 113 GLN ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071956 restraints weight = 18752.768| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.52 r_work: 0.2990 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9606 Z= 0.166 Angle : 0.749 10.473 13065 Z= 0.371 Chirality : 0.044 0.168 1497 Planarity : 0.005 0.064 1626 Dihedral : 6.313 67.117 1735 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.81 % Favored : 94.74 % Rotamer: Outliers : 2.26 % Allowed : 28.29 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.23), residues: 1122 helix: 0.11 (0.41), residues: 174 sheet: 0.13 (0.29), residues: 318 loop : -1.46 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 176 TYR 0.020 0.001 TYR H 32 PHE 0.014 0.001 PHE I 54 TRP 0.022 0.001 TRP H 107 HIS 0.002 0.001 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9573) covalent geometry : angle 0.73871 (12975) SS BOND : bond 0.00227 ( 9) SS BOND : angle 0.89615 ( 18) hydrogen bonds : bond 0.03661 ( 308) hydrogen bonds : angle 4.74403 ( 804) link_ALPHA1-3 : bond 0.00603 ( 3) link_ALPHA1-3 : angle 1.44898 ( 9) link_ALPHA1-6 : bond 0.01312 ( 3) link_ALPHA1-6 : angle 2.12137 ( 9) link_BETA1-4 : bond 0.00419 ( 12) link_BETA1-4 : angle 1.70791 ( 36) link_NAG-ASN : bond 0.00362 ( 6) link_NAG-ASN : angle 1.84559 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3292.74 seconds wall clock time: 56 minutes 45.08 seconds (3405.08 seconds total)