Starting phenix.real_space_refine on Fri Jul 3 04:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.map" model { file = "/net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x3j_66501/07_2026/9x3j_66501.cif" } resolution = 3.47 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= 0.001 sd= 0.022 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 42 5.16 5 C 7401 2.51 5 N 1944 2.21 5 O 2292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11679 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1996 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 3 Chain: "I" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 807 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1996 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 3 Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 807 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1996 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 3 Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 965 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 807 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" 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: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.91, per 1000 atoms: 0.25 Number of scatterers: 11679 At special positions: 0 Unit cell: (145.27, 135.78, 96.36, 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 42 16.00 O 2292 8.00 N 1944 7.00 C 7401 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 492 " - pdb=" SG CYS A 537 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 492 " - pdb=" SG CYS B 537 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 127 " distance=2.03 Simple disulfide: pdb=" SG CYS E 492 " - pdb=" SG CYS E 537 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " 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 H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA K 3 " - " MAN K 6 " " MAN K 4 " - " MAN K 5 " " BMA N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA N 3 " - " MAN N 4 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 701 " - " ASN A 179 " " NAG B 701 " - " ASN B 179 " " NAG E 701 " - " ASN E 179 " " NAG H 1 " - " ASN A 544 " " NAG J 1 " - " ASN A 102 " " NAG K 1 " - " ASN E 544 " " NAG L 1 " - " ASN E 102 " " NAG N 1 " - " ASN B 544 " " NAG O 1 " - " ASN B 102 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 419.2 milliseconds 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 35 sheets defined 12.4% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.550A pdb=" N LYS A 66 " --> pdb=" O THR A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 533 through 557 removed outlier: 3.578A pdb=" N CYS A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 576 removed outlier: 3.711A pdb=" N ARG A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE A 571 " --> pdb=" O ASN A 567 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.691A pdb=" N THR I 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.566A pdb=" N LYS B 66 " --> pdb=" O THR B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 533 through 557 removed outlier: 4.876A pdb=" N LYS B 548 " --> pdb=" O ASN B 544 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 549 " --> pdb=" O GLN B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.796A pdb=" N THR C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 53 No H-bonds generated for 'chain 'E' and resid 51 through 53' Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.557A pdb=" N LYS E 66 " --> pdb=" O THR E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 180 through 187 Processing helix chain 'E' and resid 533 through 557 removed outlier: 3.526A pdb=" N CYS E 537 " --> pdb=" O ASN E 533 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS E 548 " --> pdb=" O ASN E 544 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER E 549 " --> pdb=" O GLN E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 569 removed outlier: 3.619A pdb=" N ARG E 568 " --> pdb=" O SER E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 576 removed outlier: 3.509A pdb=" N ALA E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.749A pdb=" N THR F 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 removed outlier: 6.835A pdb=" N VAL A 30 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 473 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 106 removed outlier: 7.066A pdb=" N CYS A 100 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE A 133 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASN A 102 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLY A 135 " --> pdb=" O ASN A 102 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER A 104 " --> pdb=" O GLY A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 501 Processing sheet with id=AA6, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.923A pdb=" N CYS I 22 " --> pdb=" O LEU I 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.923A pdb=" N CYS I 22 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.668A pdb=" N THR I 120 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY I 51 " --> pdb=" O TRP I 38 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG I 40 " --> pdb=" O TRP I 49 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TRP I 49 " --> pdb=" O ARG I 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.668A pdb=" N THR I 120 " --> pdb=" O TYR I 95 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR I 115 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG I 101 " --> pdb=" O PHE I 113 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE I 113 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL I 103 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N SER I 111 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 9 through 12 removed outlier: 6.768A pdb=" N VAL M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.923A pdb=" N SER M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 91 through 93 removed outlier: 3.520A pdb=" N VAL M 102 " --> pdb=" O SER M 92 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 56 removed outlier: 6.824A pdb=" N VAL B 30 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 473 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 59 through 61 removed outlier: 6.697A pdb=" N THR B 88 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 81 Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 106 removed outlier: 7.098A pdb=" N CYS B 100 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE B 133 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN B 102 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY B 135 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER B 104 " --> pdb=" O GLY B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 499 through 501 removed outlier: 3.506A pdb=" N THR B 500 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.919A pdb=" N CYS C 22 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 79 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.652A pdb=" N THR C 120 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY C 51 " --> pdb=" O TRP C 38 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.652A pdb=" N THR C 120 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N CYS C 97 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N TRP C 116 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ARG C 99 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 112 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL C 103 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU C 110 " --> pdb=" O VAL C 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.789A pdb=" N VAL D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP D 37 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.864A pdb=" N SER D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.535A pdb=" N VAL D 102 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 55 through 56 removed outlier: 6.812A pdb=" N VAL E 30 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 59 through 61 Processing sheet with id=AC8, first strand: chain 'E' and resid 78 through 81 Processing sheet with id=AC9, first strand: chain 'E' and resid 100 through 106 removed outlier: 7.013A pdb=" N CYS E 100 " --> pdb=" O HIS E 131 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE E 133 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN E 102 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY E 135 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER E 104 " --> pdb=" O GLY E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 499 through 501 removed outlier: 3.614A pdb=" N THR E 500 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.891A pdb=" N CYS F 22 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.891A pdb=" N CYS F 22 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 79 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.667A pdb=" N THR F 120 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY F 51 " --> pdb=" O TRP F 38 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG F 40 " --> pdb=" O TRP F 49 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TRP F 49 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.667A pdb=" N THR F 120 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR F 115 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ARG F 101 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 113 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL F 103 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N SER F 111 " --> pdb=" O VAL F 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.743A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 18 through 23 removed outlier: 3.875A pdb=" N SER G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.547A pdb=" N VAL G 102 " --> pdb=" O SER G 92 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 906 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: 1.90 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3639 1.34 - 1.46: 2464 1.46 - 1.58: 5768 1.58 - 1.69: 3 1.69 - 1.81: 60 Bond restraints: 11934 Sorted by residual: bond pdb=" C1 MAN H 5 " pdb=" O5 MAN H 5 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 MAN K 5 " pdb=" O5 MAN K 5 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.07e+00 bond pdb=" C1 MAN N 5 " pdb=" C2 MAN N 5 " ideal model delta sigma weight residual 1.526 1.582 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C1 MAN H 5 " pdb=" C2 MAN H 5 " ideal model delta sigma weight residual 1.526 1.582 -0.056 2.00e-02 2.50e+03 7.80e+00 ... (remaining 11929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15819 2.85 - 5.70: 315 5.70 - 8.54: 50 8.54 - 11.39: 8 11.39 - 14.24: 2 Bond angle restraints: 16194 Sorted by residual: angle pdb=" C LYS A 164 " pdb=" N ASP A 165 " pdb=" CA ASP A 165 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" CA LYS C 13 " pdb=" CB LYS C 13 " pdb=" CG LYS C 13 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" CA LEU I 18 " pdb=" CB LEU I 18 " pdb=" CG LEU I 18 " ideal model delta sigma weight residual 116.30 130.54 -14.24 3.50e+00 8.16e-02 1.65e+01 angle pdb=" CA ASP B 165 " pdb=" CB ASP B 165 " pdb=" CG ASP B 165 " ideal model delta sigma weight residual 112.60 116.60 -4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" N VAL B 510 " pdb=" CA VAL B 510 " pdb=" C VAL B 510 " ideal model delta sigma weight residual 113.20 109.37 3.83 9.60e-01 1.09e+00 1.59e+01 ... (remaining 16189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 6914 21.42 - 42.84: 434 42.84 - 64.25: 48 64.25 - 85.67: 50 85.67 - 107.09: 24 Dihedral angle restraints: 7470 sinusoidal: 3291 harmonic: 4179 Sorted by residual: dihedral pdb=" CA ILE A 498 " pdb=" C ILE A 498 " pdb=" N TRP A 499 " pdb=" CA TRP A 499 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE E 498 " pdb=" C ILE E 498 " pdb=" N TRP E 499 " pdb=" CA TRP E 499 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ILE B 498 " pdb=" C ILE B 498 " pdb=" N TRP B 499 " pdb=" CA TRP B 499 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 7467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1635 0.083 - 0.167: 252 0.167 - 0.250: 17 0.250 - 0.333: 12 0.333 - 0.417: 1 Chirality restraints: 1917 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 179 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB VAL B 48 " pdb=" CA VAL B 48 " pdb=" CG1 VAL B 48 " pdb=" CG2 VAL B 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CB VAL A 48 " pdb=" CA VAL A 48 " pdb=" CG1 VAL A 48 " pdb=" CG2 VAL A 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1914 not shown) Planarity restraints: 2010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 179 " 0.001 2.00e-02 2.50e+03 2.31e-02 6.70e+00 pdb=" CG ASN B 179 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 179 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 179 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 62 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO C 63 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 62 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO F 63 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 63 " 0.033 5.00e-02 4.00e+02 ... (remaining 2007 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3581 2.83 - 3.35: 9398 3.35 - 3.87: 18591 3.87 - 4.38: 20805 4.38 - 4.90: 37713 Nonbonded interactions: 90088 Sorted by model distance: nonbonded pdb=" OG1 THR E 61 " pdb=" OE1 GLU E 95 " model vdw 2.318 3.040 nonbonded pdb=" O LEU A 542 " pdb=" OG1 THR A 546 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR A 61 " pdb=" OE1 GLU A 95 " model vdw 2.332 3.040 nonbonded pdb=" O SER M 2 " pdb=" OG SER M 2 " model vdw 2.334 3.040 nonbonded pdb=" O SER G 2 " pdb=" OG SER G 2 " model vdw 2.334 3.040 ... (remaining 90083 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' } 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: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.063 11976 Z= 0.249 Angle : 0.989 14.237 16308 Z= 0.483 Chirality : 0.062 0.417 1917 Planarity : 0.007 0.072 2001 Dihedral : 16.527 107.088 4758 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -2.81 (0.20), residues: 1428 helix: -3.74 (0.22), residues: 192 sheet: -1.93 (0.23), residues: 462 loop : -1.19 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 56 TYR 0.029 0.002 TYR I 61 PHE 0.023 0.002 PHE I 106 TRP 0.022 0.002 TRP B 148 HIS 0.016 0.002 HIS A 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 (11934) covalent geometry : angle 0.96261 / 0.48 (16194) SS BOND : bond 0.00179 / 0.12 ( 12) SS BOND : angle 0.81617 / 0.50 ( 24) hydrogen bonds : bond 0.27974 / 17.62 ( 312) hydrogen bonds : angle 9.87203 / 6.76 ( 906) link_ALPHA1-3 : bond 0.01007 / 0.73 ( 6) link_ALPHA1-3 : angle 1.80556 / 1.20 ( 18) link_ALPHA1-6 : bond 0.00126 / 0.07 ( 3) link_ALPHA1-6 : angle 1.60724 / 1.04 ( 9) link_BETA1-4 : bond 0.00850 / 0.50 ( 12) link_BETA1-4 : angle 3.13597 / 1.94 ( 36) link_NAG-ASN : bond 0.00540 / 0.35 ( 9) link_NAG-ASN : angle 4.27804 / 2.60 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8353 (mtpp) cc_final: 0.8008 (mtmt) REVERT: A 165 ASP cc_start: 0.7464 (p0) cc_final: 0.7169 (p0) REVERT: A 503 GLU cc_start: 0.7421 (pt0) cc_final: 0.7175 (pt0) REVERT: A 505 LYS cc_start: 0.8437 (tmmt) cc_final: 0.8097 (ttpt) REVERT: A 575 LEU cc_start: 0.8338 (mt) cc_final: 0.8125 (mt) REVERT: B 164 LYS cc_start: 0.8583 (tttm) cc_final: 0.8316 (ttpt) REVERT: B 551 ASP cc_start: 0.7574 (m-30) cc_final: 0.7298 (m-30) REVERT: C 41 GLN cc_start: 0.7584 (tt0) cc_final: 0.7195 (tt0) REVERT: E 98 LYS cc_start: 0.8321 (mtpp) cc_final: 0.8103 (mtmt) REVERT: E 99 ASP cc_start: 0.7333 (m-30) cc_final: 0.7118 (m-30) REVERT: E 505 LYS cc_start: 0.8491 (tmmt) cc_final: 0.8256 (ttpt) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1092 time to fit residues: 34.9762 Evaluate side-chains 181 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 569 HIS I 41 GLN B 136 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 471 HIS B 545 GLN B 569 HIS C 58 ASN C 79 GLN E 569 HIS G 40 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111514 restraints weight = 17804.561| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.36 r_work: 0.3277 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11976 Z= 0.234 Angle : 0.720 8.066 16308 Z= 0.355 Chirality : 0.049 0.195 1917 Planarity : 0.006 0.060 2001 Dihedral : 10.827 76.007 2160 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.04 % Allowed : 10.92 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.18 (0.21), residues: 1428 helix: -2.00 (0.34), residues: 174 sheet: -1.76 (0.20), residues: 576 loop : -0.77 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 56 TYR 0.017 0.002 TYR D 93 PHE 0.026 0.002 PHE B 91 TRP 0.018 0.003 TRP I 49 HIS 0.010 0.002 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 (11934) covalent geometry : angle 0.69513 / 0.35 (16194) SS BOND : bond 0.00423 / 0.34 ( 12) SS BOND : angle 0.49841 / 0.28 ( 24) hydrogen bonds : bond 0.05163 / 3.24 ( 312) hydrogen bonds : angle 5.91536 / 4.02 ( 906) link_ALPHA1-3 : bond 0.00853 / 0.58 ( 6) link_ALPHA1-3 : angle 2.81441 / 1.54 ( 18) link_ALPHA1-6 : bond 0.00094 / 0.05 ( 3) link_ALPHA1-6 : angle 1.98108 / 1.15 ( 9) link_BETA1-4 : bond 0.00456 / 0.30 ( 12) link_BETA1-4 : angle 2.60813 / 1.66 ( 36) link_NAG-ASN : bond 0.00635 / 0.45 ( 9) link_NAG-ASN : angle 2.73022 / 1.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.8100 (p) cc_final: 0.7604 (p) REVERT: A 98 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7927 (mtmt) REVERT: A 180 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7557 (ttpp) REVERT: A 503 GLU cc_start: 0.8103 (pt0) cc_final: 0.7889 (pt0) REVERT: A 505 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8312 (ttpt) REVERT: B 161 THR cc_start: 0.8528 (t) cc_final: 0.8230 (m) REVERT: B 503 GLU cc_start: 0.8184 (pt0) cc_final: 0.7956 (pt0) REVERT: E 141 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8161 (ptpp) REVERT: E 469 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7537 (mtm110) REVERT: E 472 MET cc_start: 0.8163 (tpt) cc_final: 0.7955 (mmm) outliers start: 13 outliers final: 8 residues processed: 199 average time/residue: 0.1068 time to fit residues: 30.4475 Evaluate side-chains 193 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS A 545 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112053 restraints weight = 17860.231| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.37 r_work: 0.3277 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11976 Z= 0.179 Angle : 0.645 8.752 16308 Z= 0.314 Chirality : 0.047 0.211 1917 Planarity : 0.005 0.058 2001 Dihedral : 6.769 43.161 2160 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.12 % Allowed : 14.94 % Favored : 83.94 % 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: -1.81 (0.21), residues: 1428 helix: -1.34 (0.38), residues: 171 sheet: -1.49 (0.21), residues: 570 loop : -0.69 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 541 TYR 0.013 0.002 TYR I 55 PHE 0.016 0.002 PHE B 91 TRP 0.014 0.002 TRP I 49 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (11934) covalent geometry : angle 0.62443 / 0.31 (16194) SS BOND : bond 0.00533 / 0.39 ( 12) SS BOND : angle 0.45203 / 0.27 ( 24) hydrogen bonds : bond 0.04721 / 2.98 ( 312) hydrogen bonds : angle 5.39158 / 3.63 ( 906) link_ALPHA1-3 : bond 0.01204 / 0.82 ( 6) link_ALPHA1-3 : angle 2.00654 / 1.20 ( 18) link_ALPHA1-6 : bond 0.00818 / 0.47 ( 3) link_ALPHA1-6 : angle 2.25377 / 1.32 ( 9) link_BETA1-4 : bond 0.00623 / 0.42 ( 12) link_BETA1-4 : angle 2.49421 / 1.55 ( 36) link_NAG-ASN : bond 0.00449 / 0.31 ( 9) link_NAG-ASN : angle 2.21219 / 1.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 92 THR cc_start: 0.8084 (p) cc_final: 0.7647 (p) REVERT: A 180 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7546 (ttpp) REVERT: A 503 GLU cc_start: 0.8111 (pt0) cc_final: 0.7909 (pt0) REVERT: A 505 LYS cc_start: 0.8569 (tmmt) cc_final: 0.8355 (ttpp) REVERT: B 161 THR cc_start: 0.8512 (t) cc_final: 0.8279 (m) REVERT: E 141 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8114 (ptpp) REVERT: E 469 ARG cc_start: 0.7792 (mtm110) cc_final: 0.7579 (mtm110) REVERT: E 472 MET cc_start: 0.8070 (tpt) cc_final: 0.7828 (mmm) REVERT: E 551 ASP cc_start: 0.7510 (m-30) cc_final: 0.7173 (m-30) outliers start: 14 outliers final: 12 residues processed: 197 average time/residue: 0.1029 time to fit residues: 28.8595 Evaluate side-chains 201 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 79 optimal weight: 0.0770 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 128 optimal weight: 0.0870 chunk 140 optimal weight: 6.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113876 restraints weight = 17752.378| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.37 r_work: 0.3290 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11976 Z= 0.152 Angle : 0.600 9.767 16308 Z= 0.294 Chirality : 0.046 0.182 1917 Planarity : 0.005 0.055 2001 Dihedral : 5.621 34.498 2160 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.53 % Allowed : 16.87 % Favored : 81.61 % 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: -1.57 (0.22), residues: 1428 helix: -1.03 (0.40), residues: 171 sheet: -1.29 (0.21), residues: 570 loop : -0.62 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 538 TYR 0.012 0.001 TYR I 55 PHE 0.017 0.002 PHE E 187 TRP 0.012 0.001 TRP I 49 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11934) covalent geometry : angle 0.58240 / 0.29 (16194) SS BOND : bond 0.00394 / 0.33 ( 12) SS BOND : angle 0.43707 / 0.27 ( 24) hydrogen bonds : bond 0.04066 / 2.59 ( 312) hydrogen bonds : angle 5.11864 / 3.43 ( 906) link_ALPHA1-3 : bond 0.01315 / 0.88 ( 6) link_ALPHA1-3 : angle 1.90683 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00353 / 0.20 ( 3) link_ALPHA1-6 : angle 1.73642 / 1.09 ( 9) link_BETA1-4 : bond 0.00538 / 0.36 ( 12) link_BETA1-4 : angle 2.15570 / 1.35 ( 36) link_NAG-ASN : bond 0.00415 / 0.29 ( 9) link_NAG-ASN : angle 1.98593 / 1.35 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.8084 (p) cc_final: 0.7657 (p) REVERT: A 505 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8319 (ttpp) REVERT: I 40 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6453 (ptp90) REVERT: B 161 THR cc_start: 0.8502 (t) cc_final: 0.8283 (m) REVERT: B 503 GLU cc_start: 0.8136 (pt0) cc_final: 0.7931 (pt0) REVERT: B 541 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.6967 (mtm-85) REVERT: E 469 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7560 (mtm110) REVERT: E 503 GLU cc_start: 0.7995 (pt0) cc_final: 0.7721 (pt0) REVERT: E 551 ASP cc_start: 0.7519 (m-30) cc_final: 0.7216 (m-30) outliers start: 19 outliers final: 17 residues processed: 201 average time/residue: 0.1074 time to fit residues: 30.6189 Evaluate side-chains 199 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 HIS A 545 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113396 restraints weight = 17760.180| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.37 r_work: 0.3297 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11976 Z= 0.151 Angle : 0.591 9.831 16308 Z= 0.291 Chirality : 0.046 0.182 1917 Planarity : 0.004 0.052 2001 Dihedral : 5.402 31.045 2160 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 17.51 % Favored : 80.80 % 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: -1.39 (0.22), residues: 1428 helix: -0.85 (0.41), residues: 171 sheet: -1.14 (0.22), residues: 570 loop : -0.56 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 538 TYR 0.012 0.001 TYR I 55 PHE 0.014 0.002 PHE B 91 TRP 0.010 0.001 TRP C 49 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11934) covalent geometry : angle 0.57575 / 0.29 (16194) SS BOND : bond 0.00322 / 0.26 ( 12) SS BOND : angle 0.47247 / 0.29 ( 24) hydrogen bonds : bond 0.03979 / 2.54 ( 312) hydrogen bonds : angle 5.02100 / 3.37 ( 906) link_ALPHA1-3 : bond 0.01175 / 0.79 ( 6) link_ALPHA1-3 : angle 1.88652 / 1.10 ( 18) link_ALPHA1-6 : bond 0.00477 / 0.27 ( 3) link_ALPHA1-6 : angle 1.61572 / 1.06 ( 9) link_BETA1-4 : bond 0.00518 / 0.35 ( 12) link_BETA1-4 : angle 1.97375 / 1.24 ( 36) link_NAG-ASN : bond 0.00364 / 0.25 ( 9) link_NAG-ASN : angle 1.87731 / 1.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 THR cc_start: 0.8070 (p) cc_final: 0.7670 (p) REVERT: A 496 LEU cc_start: 0.8672 (tp) cc_final: 0.8359 (tp) REVERT: A 503 GLU cc_start: 0.8136 (pt0) cc_final: 0.7882 (pt0) REVERT: A 505 LYS cc_start: 0.8527 (tmmt) cc_final: 0.8308 (tttp) REVERT: I 40 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6470 (ptp90) REVERT: B 541 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.6958 (mtm-85) REVERT: E 503 GLU cc_start: 0.7976 (pt0) cc_final: 0.7698 (pt0) REVERT: E 551 ASP cc_start: 0.7536 (m-30) cc_final: 0.7214 (m-30) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 0.1084 time to fit residues: 29.9851 Evaluate side-chains 185 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 133 optimal weight: 0.0770 chunk 129 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113683 restraints weight = 17728.796| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.37 r_work: 0.3282 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11976 Z= 0.154 Angle : 0.604 10.089 16308 Z= 0.295 Chirality : 0.046 0.185 1917 Planarity : 0.004 0.051 2001 Dihedral : 5.203 29.071 2160 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.61 % Allowed : 17.99 % Favored : 80.40 % 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: -1.30 (0.22), residues: 1428 helix: -0.86 (0.41), residues: 174 sheet: -1.01 (0.22), residues: 570 loop : -0.54 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 469 TYR 0.012 0.001 TYR I 55 PHE 0.015 0.002 PHE B 91 TRP 0.010 0.001 TRP I 49 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (11934) covalent geometry : angle 0.59021 / 0.29 (16194) SS BOND : bond 0.00315 / 0.24 ( 12) SS BOND : angle 0.45271 / 0.27 ( 24) hydrogen bonds : bond 0.03950 / 2.54 ( 312) hydrogen bonds : angle 4.96283 / 3.33 ( 906) link_ALPHA1-3 : bond 0.01169 / 0.78 ( 6) link_ALPHA1-3 : angle 1.84469 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00446 / 0.25 ( 3) link_ALPHA1-6 : angle 1.58367 / 1.05 ( 9) link_BETA1-4 : bond 0.00488 / 0.33 ( 12) link_BETA1-4 : angle 1.87953 / 1.18 ( 36) link_NAG-ASN : bond 0.00345 / 0.24 ( 9) link_NAG-ASN : angle 1.82729 / 1.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8088 (mtmm) REVERT: A 92 THR cc_start: 0.8092 (p) cc_final: 0.7702 (p) REVERT: A 496 LEU cc_start: 0.8679 (tp) cc_final: 0.8393 (tp) REVERT: A 503 GLU cc_start: 0.8129 (pt0) cc_final: 0.7877 (pt0) REVERT: A 505 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8317 (tttp) REVERT: I 40 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6469 (ptp90) REVERT: E 503 GLU cc_start: 0.7944 (pt0) cc_final: 0.7672 (pt0) REVERT: E 551 ASP cc_start: 0.7546 (m-30) cc_final: 0.7226 (m-30) outliers start: 20 outliers final: 18 residues processed: 188 average time/residue: 0.1177 time to fit residues: 31.2025 Evaluate side-chains 191 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.9980 chunk 63 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 122 optimal weight: 0.0570 chunk 32 optimal weight: 0.0870 chunk 103 optimal weight: 0.4980 chunk 110 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.0470 overall best weight: 0.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.116031 restraints weight = 17690.671| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.38 r_work: 0.3349 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11976 Z= 0.090 Angle : 0.548 10.225 16308 Z= 0.266 Chirality : 0.044 0.169 1917 Planarity : 0.004 0.048 2001 Dihedral : 4.774 26.889 2160 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.04 % Allowed : 18.71 % Favored : 80.24 % 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: -0.91 (0.22), residues: 1428 helix: -0.14 (0.42), residues: 171 sheet: -0.87 (0.22), residues: 579 loop : -0.28 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 469 TYR 0.006 0.001 TYR G 51 PHE 0.013 0.001 PHE F 106 TRP 0.011 0.001 TRP E 499 HIS 0.002 0.000 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (11934) covalent geometry : angle 0.53479 / 0.26 (16194) SS BOND : bond 0.00288 / 0.23 ( 12) SS BOND : angle 0.48850 / 0.31 ( 24) hydrogen bonds : bond 0.03251 / 2.14 ( 312) hydrogen bonds : angle 4.76332 / 3.18 ( 906) link_ALPHA1-3 : bond 0.01105 / 0.73 ( 6) link_ALPHA1-3 : angle 1.68093 / 1.03 ( 18) link_ALPHA1-6 : bond 0.00471 / 0.27 ( 3) link_ALPHA1-6 : angle 1.52596 / 1.02 ( 9) link_BETA1-4 : bond 0.00514 / 0.35 ( 12) link_BETA1-4 : angle 1.78221 / 1.13 ( 36) link_NAG-ASN : bond 0.00467 / 0.33 ( 9) link_NAG-ASN : angle 1.55792 / 1.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LEU cc_start: 0.8583 (tp) cc_final: 0.8316 (tp) REVERT: A 503 GLU cc_start: 0.8075 (pt0) cc_final: 0.7812 (pt0) REVERT: E 58 MET cc_start: 0.8275 (mtp) cc_final: 0.7908 (mtp) REVERT: E 92 THR cc_start: 0.8092 (p) cc_final: 0.7740 (p) REVERT: E 176 LEU cc_start: 0.8364 (mt) cc_final: 0.8162 (mp) REVERT: E 500 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.8115 (p) REVERT: E 503 GLU cc_start: 0.7869 (pt0) cc_final: 0.7559 (pt0) REVERT: E 551 ASP cc_start: 0.7450 (m-30) cc_final: 0.7047 (m-30) outliers start: 13 outliers final: 9 residues processed: 184 average time/residue: 0.1020 time to fit residues: 27.4191 Evaluate side-chains 176 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 495 SER Chi-restraints excluded: chain B residue 564 SER Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 40 GLN B 56 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.131145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112543 restraints weight = 17653.281| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.36 r_work: 0.3274 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11976 Z= 0.254 Angle : 0.679 10.268 16308 Z= 0.334 Chirality : 0.048 0.196 1917 Planarity : 0.005 0.051 2001 Dihedral : 5.237 25.330 2160 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.77 % Allowed : 18.55 % Favored : 79.68 % 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 (0.22), residues: 1428 helix: -0.78 (0.41), residues: 174 sheet: -0.86 (0.22), residues: 570 loop : -0.48 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 538 TYR 0.020 0.002 TYR I 55 PHE 0.027 0.002 PHE B 91 TRP 0.014 0.002 TRP I 116 HIS 0.009 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (11934) covalent geometry : angle 0.66684 / 0.33 (16194) SS BOND : bond 0.00399 / 0.30 ( 12) SS BOND : angle 0.62429 / 0.38 ( 24) hydrogen bonds : bond 0.04581 / 2.92 ( 312) hydrogen bonds : angle 5.06602 / 3.43 ( 906) link_ALPHA1-3 : bond 0.01037 / 0.69 ( 6) link_ALPHA1-3 : angle 1.93877 / 1.15 ( 18) link_ALPHA1-6 : bond 0.00464 / 0.26 ( 3) link_ALPHA1-6 : angle 1.56669 / 1.05 ( 9) link_BETA1-4 : bond 0.00443 / 0.30 ( 12) link_BETA1-4 : angle 1.82828 / 1.14 ( 36) link_NAG-ASN : bond 0.00276 / 0.18 ( 9) link_NAG-ASN : angle 1.86584 / 1.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 496 LEU cc_start: 0.8666 (tp) cc_final: 0.8366 (tp) REVERT: E 497 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7101 (tpp80) REVERT: E 526 MET cc_start: 0.7922 (tpt) cc_final: 0.6956 (tpt) REVERT: E 551 ASP cc_start: 0.7581 (m-30) cc_final: 0.7265 (m-30) outliers start: 22 outliers final: 18 residues processed: 189 average time/residue: 0.1024 time to fit residues: 27.2995 Evaluate side-chains 189 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 101 optimal weight: 0.0670 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 40 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113469 restraints weight = 17575.356| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.42 r_work: 0.3305 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11976 Z= 0.131 Angle : 0.601 10.522 16308 Z= 0.292 Chirality : 0.045 0.182 1917 Planarity : 0.004 0.050 2001 Dihedral : 4.894 24.208 2160 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.04 % Allowed : 20.08 % Favored : 78.88 % 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: -1.04 (0.22), residues: 1428 helix: -0.57 (0.42), residues: 174 sheet: -0.81 (0.23), residues: 534 loop : -0.47 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 469 TYR 0.010 0.001 TYR I 55 PHE 0.013 0.001 PHE B 91 TRP 0.010 0.001 TRP E 512 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (11934) covalent geometry : angle 0.58884 / 0.29 (16194) SS BOND : bond 0.00286 / 0.21 ( 12) SS BOND : angle 0.41322 / 0.26 ( 24) hydrogen bonds : bond 0.03809 / 2.46 ( 312) hydrogen bonds : angle 4.89703 / 3.30 ( 906) link_ALPHA1-3 : bond 0.01030 / 0.69 ( 6) link_ALPHA1-3 : angle 1.75773 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00444 / 0.25 ( 3) link_ALPHA1-6 : angle 1.53087 / 1.03 ( 9) link_BETA1-4 : bond 0.00472 / 0.32 ( 12) link_BETA1-4 : angle 1.73437 / 1.09 ( 36) link_NAG-ASN : bond 0.00352 / 0.24 ( 9) link_NAG-ASN : angle 1.69786 / 1.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.439 Fit side-chains REVERT: A 496 LEU cc_start: 0.8655 (tp) cc_final: 0.8370 (tp) REVERT: A 503 GLU cc_start: 0.8107 (pt0) cc_final: 0.7841 (pt0) REVERT: I 40 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6522 (ptp-170) REVERT: E 141 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8052 (ptmm) REVERT: E 551 ASP cc_start: 0.7510 (m-30) cc_final: 0.7207 (m-30) outliers start: 13 outliers final: 10 residues processed: 189 average time/residue: 0.1107 time to fit residues: 29.4885 Evaluate side-chains 189 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 70 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 overall best weight: 0.2838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114530 restraints weight = 17671.684| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.42 r_work: 0.3321 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11976 Z= 0.106 Angle : 0.585 10.410 16308 Z= 0.283 Chirality : 0.045 0.179 1917 Planarity : 0.004 0.050 2001 Dihedral : 4.697 22.813 2160 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.04 % Allowed : 20.56 % Favored : 78.39 % 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: -0.76 (0.23), residues: 1428 helix: 0.01 (0.42), residues: 171 sheet: -0.67 (0.22), residues: 567 loop : -0.31 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 469 TYR 0.008 0.001 TYR I 55 PHE 0.012 0.001 PHE F 106 TRP 0.012 0.001 TRP C 109 HIS 0.003 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (11934) covalent geometry : angle 0.57360 / 0.28 (16194) SS BOND : bond 0.00211 / 0.16 ( 12) SS BOND : angle 0.41869 / 0.26 ( 24) hydrogen bonds : bond 0.03546 / 2.32 ( 312) hydrogen bonds : angle 4.79529 / 3.23 ( 906) link_ALPHA1-3 : bond 0.00997 / 0.66 ( 6) link_ALPHA1-3 : angle 1.68793 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00469 / 0.27 ( 3) link_ALPHA1-6 : angle 1.50764 / 1.01 ( 9) link_BETA1-4 : bond 0.00477 / 0.32 ( 12) link_BETA1-4 : angle 1.71680 / 1.08 ( 36) link_NAG-ASN : bond 0.00359 / 0.25 ( 9) link_NAG-ASN : angle 1.59714 / 1.11 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2856 Ramachandran restraints generated. 1428 Oldfield, 0 Emsley, 1428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 LEU cc_start: 0.8624 (tp) cc_final: 0.8319 (tp) REVERT: I 40 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6545 (ptp-170) REVERT: B 500 THR cc_start: 0.8047 (OUTLIER) cc_final: 0.7712 (p) REVERT: E 500 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8042 (p) REVERT: E 526 MET cc_start: 0.7760 (tpt) cc_final: 0.7458 (tpt) REVERT: E 551 ASP cc_start: 0.7490 (m-30) cc_final: 0.7141 (m-30) outliers start: 13 outliers final: 9 residues processed: 177 average time/residue: 0.1090 time to fit residues: 27.2833 Evaluate side-chains 178 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain I residue 40 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain F residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 114 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 127 optimal weight: 0.0270 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.113916 restraints weight = 17611.101| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.37 r_work: 0.3287 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11976 Z= 0.186 Angle : 0.632 10.330 16308 Z= 0.308 Chirality : 0.046 0.184 1917 Planarity : 0.004 0.053 2001 Dihedral : 4.890 21.905 2160 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.12 % Allowed : 20.56 % Favored : 78.31 % 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: -0.93 (0.23), residues: 1428 helix: -0.47 (0.42), residues: 174 sheet: -0.88 (0.22), residues: 591 loop : -0.17 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 469 TYR 0.014 0.002 TYR I 55 PHE 0.021 0.002 PHE B 91 TRP 0.011 0.001 TRP I 116 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11934) covalent geometry : angle 0.62054 / 0.31 (16194) SS BOND : bond 0.00365 / 0.27 ( 12) SS BOND : angle 0.51930 / 0.31 ( 24) hydrogen bonds : bond 0.04083 / 2.62 ( 312) hydrogen bonds : angle 4.93663 / 3.35 ( 906) link_ALPHA1-3 : bond 0.00903 / 0.61 ( 6) link_ALPHA1-3 : angle 1.77666 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00451 / 0.26 ( 3) link_ALPHA1-6 : angle 1.51977 / 1.03 ( 9) link_BETA1-4 : bond 0.00440 / 0.30 ( 12) link_BETA1-4 : angle 1.72257 / 1.08 ( 36) link_NAG-ASN : bond 0.00244 / 0.16 ( 9) link_NAG-ASN : angle 1.70178 / 1.17 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2943.20 seconds wall clock time: 51 minutes 14.37 seconds (3074.37 seconds total)