Starting phenix.real_space_refine on Sat Sep 12 04:45:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzm_8936/09_2026/6dzm_8936.map" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 8628 2.51 5 N 2253 2.21 5 O 2649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13584 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1781 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain breaks: 3 Chain: "D" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 912 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "G" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 920 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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 chiralities: 1 Chain: "D" 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 chiralities: 1 Restraints were copied for chains: B, C, E, F, K, L, I, J, O, Q, P, R Time building chain proxies: 2.70, per 1000 atoms: 0.20 Number of scatterers: 13584 At special positions: 0 Unit cell: (138.86, 140.17, 111.35, 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 54 16.00 O 2649 8.00 N 2253 7.00 C 8628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS D 609 " distance=2.01 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS D 601 " - pdb=" SG CYS D 608 " distance=2.02 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS E 609 " distance=2.01 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS F 609 " distance=2.01 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS E 601 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS F 601 " - pdb=" SG CYS F 608 " distance=2.02 Simple disulfide: pdb=" SG CYS K 24 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " 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 N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 403 " - " ASN A 228 " " NAG B 403 " - " ASN B 228 " " NAG C 403 " - " ASN C 228 " " NAG D 701 " - " ASN D 618 " " NAG E 701 " - " ASN E 618 " " NAG F 701 " - " ASN F 618 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 576.7 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 15.0% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.948A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.004A pdb=" N ASN D 618 " --> pdb=" O ASP D 614 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.771A pdb=" N ALA H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.947A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'E' and resid 614 through 624 removed outlier: 4.004A pdb=" N ASN E 618 " --> pdb=" O ASP E 614 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.770A pdb=" N ALA K 85 " --> pdb=" O ASP K 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 249 through 263 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.947A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA F 575 " --> pdb=" O LEU F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'F' and resid 614 through 624 removed outlier: 4.005A pdb=" N ASN F 618 " --> pdb=" O ASP F 614 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.771A pdb=" N ALA L 85 " --> pdb=" O ASP L 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY A 36 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 103 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 102 " --> pdb=" O TRP D 518 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY A 36 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 38 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.519A pdb=" N GLY A 87 " --> pdb=" O PHE A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY A 145 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS A 114 " --> pdb=" O GLY A 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN A 235 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 242 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 237 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER H 66 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 54 through 55 removed outlier: 6.561A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AA9, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.902A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA G 93 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY B 36 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 103 " --> pdb=" O GLY B 67 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 102 " --> pdb=" O TRP E 518 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY B 36 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 38 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.519A pdb=" N GLY B 87 " --> pdb=" O PHE B 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY B 145 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS B 114 " --> pdb=" O GLY B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN B 235 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL B 242 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 237 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER K 66 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 54 through 55 removed outlier: 6.560A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 18 through 22 Processing sheet with id=AB9, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.902A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 93 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY C 36 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 103 " --> pdb=" O GLY C 67 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 102 " --> pdb=" O TRP F 518 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.603A pdb=" N GLY C 36 " --> pdb=" O PHE C 183 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 38 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 86 through 87 removed outlier: 3.520A pdb=" N GLY C 87 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 109 through 115 removed outlier: 6.319A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY C 145 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LYS C 114 " --> pdb=" O GLY C 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 233 through 237 removed outlier: 6.180A pdb=" N GLN C 235 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 242 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 237 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.643A pdb=" N SER L 66 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.561A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 18 through 22 Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.901A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 999 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: 2.03 Time building geometry restraints manager: 1.25 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: 4274 1.34 - 1.46: 3602 1.46 - 1.58: 5972 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 13914 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" C1 NAG F 701 " pdb=" O5 NAG F 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" C1 NAG E 701 " pdb=" O5 NAG E 701 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.47e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 13909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 17045 1.44 - 2.88: 1553 2.88 - 4.32: 198 4.32 - 5.76: 98 5.76 - 7.20: 36 Bond angle restraints: 18930 Sorted by residual: angle pdb=" C ASN I 82A" pdb=" N SER I 82B" pdb=" CA SER I 82B" ideal model delta sigma weight residual 121.31 126.11 -4.80 1.49e+00 4.50e-01 1.04e+01 angle pdb=" C ASN G 82A" pdb=" N SER G 82B" pdb=" CA SER G 82B" ideal model delta sigma weight residual 121.56 126.15 -4.59 1.56e+00 4.11e-01 8.66e+00 angle pdb=" C ASN J 82A" pdb=" N SER J 82B" pdb=" CA SER J 82B" ideal model delta sigma weight residual 121.56 126.13 -4.57 1.56e+00 4.11e-01 8.59e+00 angle pdb=" N GLY F 528 " pdb=" CA GLY F 528 " pdb=" C GLY F 528 " ideal model delta sigma weight residual 113.18 106.49 6.69 2.37e+00 1.78e-01 7.98e+00 angle pdb=" N GLY D 528 " pdb=" CA GLY D 528 " pdb=" C GLY D 528 " ideal model delta sigma weight residual 113.18 106.50 6.68 2.37e+00 1.78e-01 7.95e+00 ... (remaining 18925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 7547 15.11 - 30.21: 295 30.21 - 45.31: 69 45.31 - 60.42: 18 60.42 - 75.52: 9 Dihedral angle restraints: 7938 sinusoidal: 3093 harmonic: 4845 Sorted by residual: dihedral pdb=" CA TYR D 534 " pdb=" C TYR D 534 " pdb=" N PHE D 535 " pdb=" CA PHE D 535 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR E 534 " pdb=" C TYR E 534 " pdb=" N PHE E 535 " pdb=" CA PHE E 535 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TYR F 534 " pdb=" C TYR F 534 " pdb=" N PHE F 535 " pdb=" CA PHE F 535 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 7935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1512 0.047 - 0.095: 441 0.095 - 0.142: 175 0.142 - 0.190: 29 0.190 - 0.237: 9 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN E 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN D 563 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN F 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 2163 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 618 " -0.027 2.00e-02 2.50e+03 2.53e-02 8.03e+00 pdb=" CG ASN F 618 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN F 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN F 618 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 618 " 0.027 2.00e-02 2.50e+03 2.52e-02 7.96e+00 pdb=" CG ASN D 618 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 618 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN D 618 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 618 " -0.027 2.00e-02 2.50e+03 2.51e-02 7.87e+00 pdb=" CG ASN E 618 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN E 618 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 618 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG E 701 " -0.029 2.00e-02 2.50e+03 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 312 2.63 - 3.19: 13107 3.19 - 3.76: 21029 3.76 - 4.33: 29430 4.33 - 4.90: 46464 Nonbonded interactions: 110342 Sorted by model distance: nonbonded pdb=" O4 NAG N 1 " pdb=" O7 NAG N 2 " model vdw 2.058 3.040 nonbonded pdb=" O4 NAG R 1 " pdb=" O7 NAG R 2 " model vdw 2.058 3.040 nonbonded pdb=" O4 NAG P 1 " pdb=" O7 NAG P 2 " model vdw 2.058 3.040 nonbonded pdb=" O3 NAG P 2 " pdb=" O5 BMA P 3 " model vdw 2.203 3.040 nonbonded pdb=" O3 NAG R 2 " pdb=" O5 BMA R 3 " model vdw 2.203 3.040 ... (remaining 110337 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13962 Z= 0.351 Angle : 1.049 21.036 19053 Z= 0.526 Chirality : 0.054 0.237 2166 Planarity : 0.006 0.049 2382 Dihedral : 9.605 75.524 4779 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.61 % Favored : 86.39 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -4.76 (0.18), residues: 1653 helix: -2.49 (0.28), residues: 207 sheet: -3.57 (0.19), residues: 441 loop : -3.23 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 85 TYR 0.025 0.002 TYR L 92 PHE 0.027 0.003 PHE A 160 TRP 0.021 0.003 TRP F 597 HIS 0.009 0.003 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00782 / 0.35 (13914) covalent geometry : angle 0.95646 / 0.49 (18930) SS BOND : bond 0.01136 / 0.53 ( 21) SS BOND : angle 7.07991 / 4.36 ( 42) hydrogen bonds : bond 0.23347 / 15.75 ( 387) hydrogen bonds : angle 10.40260 / 7.28 ( 999) link_ALPHA1-3 : bond 0.00466 / 0.21 ( 3) link_ALPHA1-3 : angle 1.86241 / 0.98 ( 9) link_ALPHA1-6 : bond 0.00515 / 0.24 ( 3) link_ALPHA1-6 : angle 1.67791 / 0.89 ( 9) link_BETA1-4 : bond 0.00439 / 0.18 ( 9) link_BETA1-4 : angle 5.46634 / 2.99 ( 27) link_NAG-ASN : bond 0.02158 / 1.15 ( 12) link_NAG-ASN : angle 4.35536 / 2.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8833 (mt) cc_final: 0.8312 (mm) REVERT: A 39 HIS cc_start: 0.8481 (t70) cc_final: 0.8191 (t70) REVERT: A 163 ASP cc_start: 0.8933 (t0) cc_final: 0.7780 (t0) REVERT: D 567 GLN cc_start: 0.9319 (tt0) cc_final: 0.8815 (tt0) REVERT: D 588 LYS cc_start: 0.9030 (tppt) cc_final: 0.8733 (tttm) REVERT: D 591 ASP cc_start: 0.8806 (m-30) cc_final: 0.8500 (m-30) REVERT: H 87 TYR cc_start: 0.8474 (m-10) cc_final: 0.8204 (m-10) REVERT: G 32 TYR cc_start: 0.8878 (m-80) cc_final: 0.7955 (m-80) REVERT: B 33 ILE cc_start: 0.8871 (mt) cc_final: 0.8327 (mm) REVERT: B 162 TYR cc_start: 0.8707 (m-80) cc_final: 0.8479 (m-10) REVERT: B 163 ASP cc_start: 0.8864 (t0) cc_final: 0.8006 (t0) REVERT: E 588 LYS cc_start: 0.9165 (tppt) cc_final: 0.8943 (tttp) REVERT: E 591 ASP cc_start: 0.8765 (m-30) cc_final: 0.8294 (m-30) REVERT: C 33 ILE cc_start: 0.8816 (mt) cc_final: 0.8153 (mt) REVERT: C 163 ASP cc_start: 0.8743 (t0) cc_final: 0.7269 (t0) REVERT: F 567 GLN cc_start: 0.9316 (tt0) cc_final: 0.8978 (tt0) REVERT: F 588 LYS cc_start: 0.9110 (tppt) cc_final: 0.8804 (tttp) REVERT: F 591 ASP cc_start: 0.8967 (m-30) cc_final: 0.8649 (m-30) REVERT: L 87 TYR cc_start: 0.8412 (m-10) cc_final: 0.8203 (m-10) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1679 time to fit residues: 70.4011 Evaluate side-chains 143 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN A 224 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN C 44 GLN C 224 ASN F 595 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.048070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040009 restraints weight = 111936.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.041119 restraints weight = 71269.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.041914 restraints weight = 51002.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042501 restraints weight = 39508.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042858 restraints weight = 32467.892| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13962 Z= 0.179 Angle : 0.822 12.041 19053 Z= 0.407 Chirality : 0.048 0.256 2166 Planarity : 0.007 0.084 2382 Dihedral : 7.333 80.444 1827 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.35 % Allowed : 1.19 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.68 (0.19), residues: 1653 helix: -1.04 (0.33), residues: 213 sheet: -3.12 (0.19), residues: 438 loop : -2.50 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 19 TYR 0.019 0.002 TYR G 79 PHE 0.017 0.002 PHE J 67 TRP 0.026 0.002 TRP J 103 HIS 0.005 0.001 HIS J 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (13914) covalent geometry : angle 0.79717 / 0.40 (18930) SS BOND : bond 0.00454 / 0.23 ( 21) SS BOND : angle 1.89809 / 1.21 ( 42) hydrogen bonds : bond 0.04920 / 3.39 ( 387) hydrogen bonds : angle 7.09476 / 4.99 ( 999) link_ALPHA1-3 : bond 0.00827 / 0.40 ( 3) link_ALPHA1-3 : angle 1.17186 / 0.62 ( 9) link_ALPHA1-6 : bond 0.00728 / 0.34 ( 3) link_ALPHA1-6 : angle 1.24908 / 0.68 ( 9) link_BETA1-4 : bond 0.00505 / 0.22 ( 9) link_BETA1-4 : angle 3.04781 / 1.59 ( 27) link_NAG-ASN : bond 0.00868 / 0.46 ( 12) link_NAG-ASN : angle 3.42595 / 2.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.8977 (mt) cc_final: 0.8663 (mm) REVERT: A 49 ASP cc_start: 0.8835 (p0) cc_final: 0.8460 (p0) REVERT: A 163 ASP cc_start: 0.8936 (t0) cc_final: 0.8556 (t0) REVERT: D 591 ASP cc_start: 0.8933 (m-30) cc_final: 0.8594 (m-30) REVERT: D 602 HIS cc_start: 0.8993 (m-70) cc_final: 0.8717 (t70) REVERT: H 87 TYR cc_start: 0.8577 (m-10) cc_final: 0.8267 (m-80) REVERT: G 32 TYR cc_start: 0.8920 (m-80) cc_final: 0.8201 (m-80) REVERT: B 33 ILE cc_start: 0.8998 (mt) cc_final: 0.8707 (mm) REVERT: B 49 ASP cc_start: 0.8758 (p0) cc_final: 0.8343 (p0) REVERT: B 163 ASP cc_start: 0.8958 (t0) cc_final: 0.8694 (t0) REVERT: E 584 ILE cc_start: 0.8925 (pt) cc_final: 0.8677 (mp) REVERT: E 587 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8700 (mtp-110) REVERT: E 591 ASP cc_start: 0.8900 (m-30) cc_final: 0.8564 (m-30) REVERT: E 602 HIS cc_start: 0.9070 (m-70) cc_final: 0.8805 (t70) REVERT: E 618 ASN cc_start: 0.7114 (p0) cc_final: 0.6042 (t0) REVERT: K 87 TYR cc_start: 0.8732 (m-80) cc_final: 0.8296 (m-10) REVERT: I 67 PHE cc_start: 0.8861 (m-80) cc_final: 0.8654 (m-80) REVERT: I 80 LEU cc_start: 0.9793 (tp) cc_final: 0.9222 (tp) REVERT: C 33 ILE cc_start: 0.8984 (mt) cc_final: 0.8602 (mt) REVERT: C 49 ASP cc_start: 0.9045 (p0) cc_final: 0.8547 (p0) REVERT: C 163 ASP cc_start: 0.8494 (t0) cc_final: 0.8248 (t0) REVERT: F 584 ILE cc_start: 0.9164 (pt) cc_final: 0.8954 (mp) REVERT: F 587 ARG cc_start: 0.9029 (mtp-110) cc_final: 0.8715 (mtp-110) REVERT: F 591 ASP cc_start: 0.9030 (m-30) cc_final: 0.8638 (m-30) REVERT: F 602 HIS cc_start: 0.9139 (m-70) cc_final: 0.8812 (t70) REVERT: L 87 TYR cc_start: 0.8507 (m-10) cc_final: 0.8087 (m-10) REVERT: J 79 TYR cc_start: 0.8530 (m-80) cc_final: 0.8090 (m-80) outliers start: 5 outliers final: 0 residues processed: 242 average time/residue: 0.1395 time to fit residues: 46.1334 Evaluate side-chains 137 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 0.0470 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 224 ASN D 560 GLN H 38 GLN G 6 GLN B 224 ASN E 560 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN F 551 GLN F 560 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.045350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.037338 restraints weight = 117065.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.038343 restraints weight = 75313.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.039081 restraints weight = 54862.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039580 restraints weight = 43077.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.039840 restraints weight = 36042.430| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13962 Z= 0.209 Angle : 0.769 9.137 19053 Z= 0.381 Chirality : 0.047 0.280 2166 Planarity : 0.007 0.108 2382 Dihedral : 6.822 78.827 1827 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.21 % Allowed : 2.52 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.17 (0.20), residues: 1653 helix: -0.31 (0.34), residues: 213 sheet: -2.68 (0.19), residues: 462 loop : -2.27 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 85 TYR 0.019 0.002 TYR K 88 PHE 0.013 0.002 PHE G 29 TRP 0.025 0.002 TRP C 86 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (13914) covalent geometry : angle 0.75054 / 0.38 (18930) SS BOND : bond 0.01022 / 0.27 ( 21) SS BOND : angle 0.99224 / 0.56 ( 42) hydrogen bonds : bond 0.04252 / 2.93 ( 387) hydrogen bonds : angle 6.49429 / 4.62 ( 999) link_ALPHA1-3 : bond 0.00776 / 0.38 ( 3) link_ALPHA1-3 : angle 1.52911 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00832 / 0.39 ( 3) link_ALPHA1-6 : angle 1.31823 / 0.70 ( 9) link_BETA1-4 : bond 0.00677 / 0.31 ( 9) link_BETA1-4 : angle 2.73248 / 1.43 ( 27) link_NAG-ASN : bond 0.01009 / 0.40 ( 12) link_NAG-ASN : angle 2.95839 / 1.98 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 587 ARG cc_start: 0.9090 (mtp-110) cc_final: 0.8369 (ttp80) REVERT: D 591 ASP cc_start: 0.9118 (m-30) cc_final: 0.8475 (m-30) REVERT: D 602 HIS cc_start: 0.9091 (m-70) cc_final: 0.8748 (t70) REVERT: G 32 TYR cc_start: 0.8700 (m-80) cc_final: 0.8074 (m-80) REVERT: G 45 LEU cc_start: 0.9024 (mm) cc_final: 0.8710 (mm) REVERT: B 86 TRP cc_start: 0.8918 (m-10) cc_final: 0.8073 (m-90) REVERT: B 163 ASP cc_start: 0.8859 (t0) cc_final: 0.8554 (t0) REVERT: E 584 ILE cc_start: 0.9170 (pt) cc_final: 0.8918 (mp) REVERT: E 587 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8395 (ttp80) REVERT: E 591 ASP cc_start: 0.9100 (m-30) cc_final: 0.7993 (m-30) REVERT: E 602 HIS cc_start: 0.9179 (m-70) cc_final: 0.8942 (t70) REVERT: E 618 ASN cc_start: 0.7142 (p0) cc_final: 0.6417 (t160) REVERT: C 33 ILE cc_start: 0.9005 (mt) cc_final: 0.8799 (mm) REVERT: C 49 ASP cc_start: 0.8581 (p0) cc_final: 0.8250 (p0) REVERT: F 567 GLN cc_start: 0.9359 (tt0) cc_final: 0.8950 (tm-30) REVERT: F 571 LEU cc_start: 0.9257 (mt) cc_final: 0.8779 (mt) REVERT: F 587 ARG cc_start: 0.9044 (mtp-110) cc_final: 0.8807 (mtp-110) REVERT: F 591 ASP cc_start: 0.9079 (m-30) cc_final: 0.8712 (m-30) REVERT: F 595 GLN cc_start: 0.9460 (pt0) cc_final: 0.9169 (pp30) REVERT: F 602 HIS cc_start: 0.9101 (m-70) cc_final: 0.8704 (t70) REVERT: L 87 TYR cc_start: 0.8657 (m-10) cc_final: 0.8115 (m-10) REVERT: J 32 TYR cc_start: 0.9022 (m-80) cc_final: 0.8791 (m-80) outliers start: 3 outliers final: 0 residues processed: 194 average time/residue: 0.1387 time to fit residues: 37.3696 Evaluate side-chains 120 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN D 521 GLN E 521 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN J 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.043042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.035170 restraints weight = 114893.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.036182 restraints weight = 73793.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.036882 restraints weight = 53422.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037339 restraints weight = 42122.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.037726 restraints weight = 35553.980| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13962 Z= 0.262 Angle : 0.797 9.314 19053 Z= 0.397 Chirality : 0.047 0.218 2166 Planarity : 0.007 0.143 2382 Dihedral : 6.780 78.064 1827 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.85 (0.20), residues: 1653 helix: -0.19 (0.33), residues: 213 sheet: -2.33 (0.20), residues: 477 loop : -2.08 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG K 19 TYR 0.021 0.002 TYR K 87 PHE 0.019 0.002 PHE G 67 TRP 0.027 0.002 TRP G 103 HIS 0.007 0.002 HIS B 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.26 (13914) covalent geometry : angle 0.78156 / 0.39 (18930) SS BOND : bond 0.00642 / 0.21 ( 21) SS BOND : angle 0.72940 / 0.42 ( 42) hydrogen bonds : bond 0.04070 / 2.77 ( 387) hydrogen bonds : angle 6.33805 / 4.54 ( 999) link_ALPHA1-3 : bond 0.00562 / 0.25 ( 3) link_ALPHA1-3 : angle 1.56606 / 0.84 ( 9) link_ALPHA1-6 : bond 0.00563 / 0.26 ( 3) link_ALPHA1-6 : angle 1.27327 / 0.68 ( 9) link_BETA1-4 : bond 0.00348 / 0.13 ( 9) link_BETA1-4 : angle 2.83815 / 1.53 ( 27) link_NAG-ASN : bond 0.00907 / 0.35 ( 12) link_NAG-ASN : angle 2.66516 / 1.77 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 587 ARG cc_start: 0.9094 (mtp-110) cc_final: 0.8456 (ttp80) REVERT: D 591 ASP cc_start: 0.9180 (m-30) cc_final: 0.8559 (m-30) REVERT: G 32 TYR cc_start: 0.8979 (m-80) cc_final: 0.8247 (m-80) REVERT: E 567 GLN cc_start: 0.9447 (tt0) cc_final: 0.9165 (tm-30) REVERT: E 571 LEU cc_start: 0.9272 (mt) cc_final: 0.8808 (mt) REVERT: E 591 ASP cc_start: 0.9368 (m-30) cc_final: 0.8951 (m-30) REVERT: K 46 LYS cc_start: 0.9340 (pttt) cc_final: 0.9120 (ptmm) REVERT: C 99 TYR cc_start: 0.9067 (p90) cc_final: 0.8751 (p90) REVERT: F 591 ASP cc_start: 0.9267 (m-30) cc_final: 0.8781 (m-30) REVERT: J 79 TYR cc_start: 0.8463 (m-80) cc_final: 0.8174 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1393 time to fit residues: 31.6468 Evaluate side-chains 106 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 123 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 22 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.035849 restraints weight = 111567.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.036875 restraints weight = 70581.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.037620 restraints weight = 50546.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038059 restraints weight = 39323.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038431 restraints weight = 33434.303| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13962 Z= 0.140 Angle : 0.695 9.196 19053 Z= 0.342 Chirality : 0.046 0.253 2166 Planarity : 0.006 0.138 2382 Dihedral : 6.473 80.358 1827 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.07 % Allowed : 1.96 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.51 (0.20), residues: 1653 helix: 0.19 (0.35), residues: 213 sheet: -1.85 (0.22), residues: 462 loop : -2.05 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 134 TYR 0.019 0.002 TYR K 88 PHE 0.017 0.002 PHE I 67 TRP 0.018 0.001 TRP G 103 HIS 0.004 0.001 HIS F 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (13914) covalent geometry : angle 0.68351 / 0.34 (18930) SS BOND : bond 0.00267 / 0.16 ( 21) SS BOND : angle 0.59300 / 0.37 ( 42) hydrogen bonds : bond 0.03512 / 2.42 ( 387) hydrogen bonds : angle 6.03239 / 4.32 ( 999) link_ALPHA1-3 : bond 0.00677 / 0.30 ( 3) link_ALPHA1-3 : angle 1.24070 / 0.67 ( 9) link_ALPHA1-6 : bond 0.00759 / 0.35 ( 3) link_ALPHA1-6 : angle 1.34187 / 0.70 ( 9) link_BETA1-4 : bond 0.00529 / 0.24 ( 9) link_BETA1-4 : angle 2.42290 / 1.28 ( 27) link_NAG-ASN : bond 0.00738 / 0.38 ( 12) link_NAG-ASN : angle 2.16032 / 1.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8712 (mpp80) cc_final: 0.8393 (mpp80) REVERT: A 253 LEU cc_start: 0.9604 (mt) cc_final: 0.9326 (tt) REVERT: D 587 ARG cc_start: 0.9119 (mtp-110) cc_final: 0.8488 (ttp80) REVERT: D 591 ASP cc_start: 0.9180 (m-30) cc_final: 0.8575 (m-30) REVERT: G 28 THR cc_start: 0.8895 (p) cc_final: 0.8549 (p) REVERT: G 32 TYR cc_start: 0.9035 (m-80) cc_final: 0.8394 (m-80) REVERT: G 45 LEU cc_start: 0.9119 (mm) cc_final: 0.8781 (mm) REVERT: B 163 ASP cc_start: 0.9138 (t70) cc_final: 0.8882 (t0) REVERT: B 253 LEU cc_start: 0.9530 (mt) cc_final: 0.9204 (tt) REVERT: E 584 ILE cc_start: 0.9225 (pt) cc_final: 0.9004 (mp) REVERT: E 591 ASP cc_start: 0.9392 (m-30) cc_final: 0.8981 (m-30) REVERT: I 45 LEU cc_start: 0.9026 (mm) cc_final: 0.8826 (mm) REVERT: C 99 TYR cc_start: 0.8787 (p90) cc_final: 0.8464 (p90) REVERT: C 253 LEU cc_start: 0.9465 (mt) cc_final: 0.9175 (tt) REVERT: F 567 GLN cc_start: 0.9481 (tt0) cc_final: 0.9161 (tt0) REVERT: F 587 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8471 (ttp80) REVERT: F 591 ASP cc_start: 0.9297 (m-30) cc_final: 0.8634 (m-30) REVERT: L 38 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8340 (pp30) REVERT: J 32 TYR cc_start: 0.9143 (m-80) cc_final: 0.8831 (m-80) REVERT: J 79 TYR cc_start: 0.8467 (m-80) cc_final: 0.8081 (m-80) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.1537 time to fit residues: 39.2787 Evaluate side-chains 126 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 111 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 521 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 HIS L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.042527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.034625 restraints weight = 117316.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.035604 restraints weight = 74329.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.036319 restraints weight = 53625.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036790 restraints weight = 42087.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.037173 restraints weight = 35476.248| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13962 Z= 0.241 Angle : 0.754 8.971 19053 Z= 0.375 Chirality : 0.046 0.212 2166 Planarity : 0.007 0.166 2382 Dihedral : 6.525 78.608 1827 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.46 (0.21), residues: 1653 helix: 0.05 (0.33), residues: 213 sheet: -1.84 (0.21), residues: 513 loop : -1.93 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 134 TYR 0.026 0.002 TYR L 88 PHE 0.059 0.002 PHE I 67 TRP 0.023 0.002 TRP G 103 HIS 0.006 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (13914) covalent geometry : angle 0.74181 / 0.37 (18930) SS BOND : bond 0.00241 / 0.15 ( 21) SS BOND : angle 0.61167 / 0.36 ( 42) hydrogen bonds : bond 0.03807 / 2.57 ( 387) hydrogen bonds : angle 6.09253 / 4.35 ( 999) link_ALPHA1-3 : bond 0.00448 / 0.20 ( 3) link_ALPHA1-3 : angle 1.54856 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00673 / 0.31 ( 3) link_ALPHA1-6 : angle 1.33441 / 0.70 ( 9) link_BETA1-4 : bond 0.00315 / 0.15 ( 9) link_BETA1-4 : angle 2.63886 / 1.42 ( 27) link_NAG-ASN : bond 0.00882 / 0.35 ( 12) link_NAG-ASN : angle 2.17475 / 1.27 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.9601 (mt) cc_final: 0.9300 (tt) REVERT: D 587 ARG cc_start: 0.9076 (mtp-110) cc_final: 0.8518 (ttp80) REVERT: D 591 ASP cc_start: 0.9235 (m-30) cc_final: 0.8590 (m-30) REVERT: D 615 TRP cc_start: 0.7482 (t-100) cc_final: 0.7173 (t-100) REVERT: H 46 LYS cc_start: 0.9272 (ptmm) cc_final: 0.8866 (ptmm) REVERT: G 32 TYR cc_start: 0.8908 (m-80) cc_final: 0.8302 (m-80) REVERT: G 45 LEU cc_start: 0.9057 (mm) cc_final: 0.8654 (mm) REVERT: G 67 PHE cc_start: 0.8223 (m-80) cc_final: 0.7815 (m-80) REVERT: G 82 MET cc_start: 0.9143 (mmp) cc_final: 0.8570 (mmp) REVERT: B 253 LEU cc_start: 0.9526 (mt) cc_final: 0.9236 (tt) REVERT: B 255 GLN cc_start: 0.9457 (mt0) cc_final: 0.9250 (mt0) REVERT: E 591 ASP cc_start: 0.9346 (m-30) cc_final: 0.8996 (m-30) REVERT: K 46 LYS cc_start: 0.9256 (ptmm) cc_final: 0.9019 (ptmm) REVERT: I 45 LEU cc_start: 0.9144 (mm) cc_final: 0.8898 (mm) REVERT: I 82 MET cc_start: 0.8719 (mmm) cc_final: 0.8037 (mmm) REVERT: C 99 TYR cc_start: 0.9135 (p90) cc_final: 0.8561 (p90) REVERT: C 253 LEU cc_start: 0.9490 (mt) cc_final: 0.9147 (tt) REVERT: F 540 GLU cc_start: 0.7621 (tp30) cc_final: 0.7390 (tp30) REVERT: F 587 ARG cc_start: 0.9045 (mtp-110) cc_final: 0.8484 (ttp80) REVERT: F 591 ASP cc_start: 0.9258 (m-30) cc_final: 0.8634 (m-30) REVERT: L 46 LYS cc_start: 0.9324 (ptmm) cc_final: 0.8895 (ptmm) REVERT: J 32 TYR cc_start: 0.9086 (m-80) cc_final: 0.8816 (m-80) REVERT: J 79 TYR cc_start: 0.8568 (m-80) cc_final: 0.8236 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1433 time to fit residues: 33.3528 Evaluate side-chains 119 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 521 GLN E 521 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034698 restraints weight = 112635.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035712 restraints weight = 71156.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.036427 restraints weight = 50980.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036942 restraints weight = 39869.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.037239 restraints weight = 33215.651| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13962 Z= 0.176 Angle : 0.701 9.038 19053 Z= 0.346 Chirality : 0.046 0.213 2166 Planarity : 0.006 0.144 2382 Dihedral : 6.424 79.798 1827 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.25 (0.21), residues: 1653 helix: 0.18 (0.34), residues: 213 sheet: -1.60 (0.23), residues: 480 loop : -1.85 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 97 TYR 0.021 0.002 TYR K 88 PHE 0.067 0.002 PHE I 67 TRP 0.023 0.002 TRP G 103 HIS 0.011 0.001 HIS D 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (13914) covalent geometry : angle 0.68973 / 0.34 (18930) SS BOND : bond 0.00214 / 0.13 ( 21) SS BOND : angle 0.51974 / 0.32 ( 42) hydrogen bonds : bond 0.03528 / 2.40 ( 387) hydrogen bonds : angle 5.95404 / 4.26 ( 999) link_ALPHA1-3 : bond 0.00614 / 0.29 ( 3) link_ALPHA1-3 : angle 1.39259 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00667 / 0.31 ( 3) link_ALPHA1-6 : angle 1.30787 / 0.69 ( 9) link_BETA1-4 : bond 0.00373 / 0.17 ( 9) link_BETA1-4 : angle 2.43790 / 1.31 ( 27) link_NAG-ASN : bond 0.00757 / 0.35 ( 12) link_NAG-ASN : angle 1.97948 / 1.22 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8269 (mpp80) REVERT: A 163 ASP cc_start: 0.8935 (t0) cc_final: 0.8682 (t0) REVERT: A 253 LEU cc_start: 0.9619 (mt) cc_final: 0.9302 (tt) REVERT: D 587 ARG cc_start: 0.9126 (mtp-110) cc_final: 0.8506 (ttp80) REVERT: D 591 ASP cc_start: 0.9235 (m-30) cc_final: 0.8573 (m-30) REVERT: G 32 TYR cc_start: 0.9068 (m-80) cc_final: 0.8458 (m-80) REVERT: G 45 LEU cc_start: 0.9098 (mm) cc_final: 0.8547 (mm) REVERT: G 64 LYS cc_start: 0.9581 (tppt) cc_final: 0.9103 (mmtt) REVERT: B 134 ARG cc_start: 0.5846 (mpp-170) cc_final: 0.5248 (mpp-170) REVERT: B 253 LEU cc_start: 0.9542 (mt) cc_final: 0.9263 (tt) REVERT: E 561 LEU cc_start: 0.9408 (tt) cc_final: 0.9158 (tt) REVERT: E 591 ASP cc_start: 0.9355 (m-30) cc_final: 0.9028 (m-30) REVERT: I 82 MET cc_start: 0.8863 (mmm) cc_final: 0.8408 (mmm) REVERT: C 99 TYR cc_start: 0.9046 (p90) cc_final: 0.8474 (p90) REVERT: C 253 LEU cc_start: 0.9482 (mt) cc_final: 0.9149 (tt) REVERT: F 540 GLU cc_start: 0.7664 (tp30) cc_final: 0.7435 (tp30) REVERT: F 561 LEU cc_start: 0.9426 (tt) cc_final: 0.8803 (tt) REVERT: F 587 ARG cc_start: 0.9060 (mtp-110) cc_final: 0.8506 (ttp80) REVERT: F 591 ASP cc_start: 0.9251 (m-30) cc_final: 0.8629 (m-30) REVERT: L 46 LYS cc_start: 0.9330 (ptmm) cc_final: 0.9060 (pptt) REVERT: J 32 TYR cc_start: 0.9115 (m-80) cc_final: 0.8775 (m-80) REVERT: J 79 TYR cc_start: 0.8581 (m-80) cc_final: 0.8225 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1335 time to fit residues: 31.2421 Evaluate side-chains 119 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 141 optimal weight: 0.0970 chunk 57 optimal weight: 0.0070 chunk 44 optimal weight: 0.0870 chunk 127 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 521 GLN B 69 ASN E 521 GLN C 44 GLN C 69 ASN F 570 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035783 restraints weight = 109837.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036839 restraints weight = 68404.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037590 restraints weight = 48699.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.038119 restraints weight = 37901.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.038544 restraints weight = 31459.150| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13962 Z= 0.116 Angle : 0.676 9.253 19053 Z= 0.332 Chirality : 0.045 0.202 2166 Planarity : 0.005 0.070 2382 Dihedral : 6.259 82.138 1827 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.21 % Allowed : 1.47 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.12 (0.20), residues: 1653 helix: 0.35 (0.34), residues: 213 sheet: -1.45 (0.23), residues: 486 loop : -1.83 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 97 TYR 0.022 0.001 TYR K 88 PHE 0.026 0.002 PHE I 67 TRP 0.012 0.001 TRP F 518 HIS 0.004 0.001 HIS F 602 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (13914) covalent geometry : angle 0.66715 / 0.33 (18930) SS BOND : bond 0.00216 / 0.14 ( 21) SS BOND : angle 0.45202 / 0.29 ( 42) hydrogen bonds : bond 0.03431 / 2.37 ( 387) hydrogen bonds : angle 5.88471 / 4.27 ( 999) link_ALPHA1-3 : bond 0.00845 / 0.39 ( 3) link_ALPHA1-3 : angle 1.28248 / 0.69 ( 9) link_ALPHA1-6 : bond 0.00808 / 0.37 ( 3) link_ALPHA1-6 : angle 1.41759 / 0.75 ( 9) link_BETA1-4 : bond 0.00637 / 0.28 ( 9) link_BETA1-4 : angle 2.06995 / 1.11 ( 27) link_NAG-ASN : bond 0.00812 / 0.38 ( 12) link_NAG-ASN : angle 1.81198 / 1.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8624 (p90) cc_final: 0.8412 (p90) REVERT: A 130 ARG cc_start: 0.8731 (mpp80) cc_final: 0.8175 (mpp80) REVERT: A 253 LEU cc_start: 0.9521 (mt) cc_final: 0.9191 (tt) REVERT: D 587 ARG cc_start: 0.9006 (mtp-110) cc_final: 0.8473 (ttp80) REVERT: D 591 ASP cc_start: 0.9123 (m-30) cc_final: 0.8539 (m-30) REVERT: H 46 LYS cc_start: 0.9276 (ptmm) cc_final: 0.8776 (ptmm) REVERT: G 28 THR cc_start: 0.8787 (p) cc_final: 0.8432 (p) REVERT: G 32 TYR cc_start: 0.9054 (m-80) cc_final: 0.8545 (m-80) REVERT: G 45 LEU cc_start: 0.8996 (mm) cc_final: 0.8450 (mm) REVERT: G 67 PHE cc_start: 0.8078 (m-80) cc_final: 0.7557 (m-80) REVERT: G 82 MET cc_start: 0.8931 (mmp) cc_final: 0.8565 (mmp) REVERT: B 111 LEU cc_start: 0.9582 (mt) cc_final: 0.9329 (mm) REVERT: B 253 LEU cc_start: 0.9496 (mt) cc_final: 0.9255 (tt) REVERT: K 46 LYS cc_start: 0.9348 (ptmm) cc_final: 0.8905 (pptt) REVERT: K 47 LEU cc_start: 0.8670 (pp) cc_final: 0.8440 (pp) REVERT: I 82 MET cc_start: 0.8879 (mmm) cc_final: 0.8676 (mmm) REVERT: I 103 TRP cc_start: 0.8554 (m100) cc_final: 0.7705 (m100) REVERT: C 99 TYR cc_start: 0.8867 (p90) cc_final: 0.8353 (p90) REVERT: C 253 LEU cc_start: 0.9419 (mt) cc_final: 0.9083 (tt) REVERT: F 561 LEU cc_start: 0.9201 (tt) cc_final: 0.8975 (tt) REVERT: F 567 GLN cc_start: 0.9395 (tt0) cc_final: 0.9020 (tt0) REVERT: F 587 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8594 (ttp80) REVERT: F 591 ASP cc_start: 0.9191 (m-30) cc_final: 0.8595 (m-30) REVERT: F 615 TRP cc_start: 0.7250 (t-100) cc_final: 0.6958 (t-100) REVERT: L 46 LYS cc_start: 0.9211 (ptmm) cc_final: 0.8916 (pptt) REVERT: L 47 LEU cc_start: 0.8785 (pp) cc_final: 0.8527 (pp) REVERT: L 48 LEU cc_start: 0.9339 (mt) cc_final: 0.8759 (mt) REVERT: J 79 TYR cc_start: 0.8469 (m-80) cc_final: 0.8204 (m-80) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.1398 time to fit residues: 36.7287 Evaluate side-chains 134 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 521 GLN D 602 HIS ** L 38 GLN ** 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 = 0.3127 r_free = 0.3127 target = 0.042888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034845 restraints weight = 113039.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035871 restraints weight = 70887.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036576 restraints weight = 50714.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037090 restraints weight = 39679.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037428 restraints weight = 33084.868| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13962 Z= 0.134 Angle : 0.686 9.230 19053 Z= 0.338 Chirality : 0.045 0.196 2166 Planarity : 0.005 0.068 2382 Dihedral : 6.168 81.598 1827 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.07 % Allowed : 0.56 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.98 (0.21), residues: 1653 helix: 0.26 (0.35), residues: 210 sheet: -1.33 (0.22), residues: 519 loop : -1.68 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 97 TYR 0.027 0.001 TYR K 88 PHE 0.026 0.002 PHE J 100E TRP 0.018 0.001 TRP E 615 HIS 0.003 0.001 HIS I 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (13914) covalent geometry : angle 0.67822 / 0.34 (18930) SS BOND : bond 0.00185 / 0.11 ( 21) SS BOND : angle 0.44894 / 0.27 ( 42) hydrogen bonds : bond 0.03493 / 2.38 ( 387) hydrogen bonds : angle 5.89455 / 4.25 ( 999) link_ALPHA1-3 : bond 0.00737 / 0.34 ( 3) link_ALPHA1-3 : angle 1.42493 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00786 / 0.36 ( 3) link_ALPHA1-6 : angle 1.38593 / 0.74 ( 9) link_BETA1-4 : bond 0.00542 / 0.25 ( 9) link_BETA1-4 : angle 1.94783 / 1.06 ( 27) link_NAG-ASN : bond 0.00711 / 0.36 ( 12) link_NAG-ASN : angle 1.80090 / 1.14 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8720 (p90) cc_final: 0.8498 (p90) REVERT: A 130 ARG cc_start: 0.8671 (mpp80) cc_final: 0.8149 (mpp80) REVERT: A 163 ASP cc_start: 0.8536 (t70) cc_final: 0.8199 (t0) REVERT: A 253 LEU cc_start: 0.9517 (mt) cc_final: 0.9252 (tt) REVERT: D 587 ARG cc_start: 0.8974 (mtp-110) cc_final: 0.8462 (ttp80) REVERT: D 591 ASP cc_start: 0.9088 (m-30) cc_final: 0.8442 (m-30) REVERT: H 46 LYS cc_start: 0.9321 (ptmm) cc_final: 0.8879 (ptmm) REVERT: G 28 THR cc_start: 0.8796 (p) cc_final: 0.8456 (p) REVERT: G 32 TYR cc_start: 0.9034 (m-80) cc_final: 0.8479 (m-80) REVERT: G 45 LEU cc_start: 0.9019 (mm) cc_final: 0.8621 (mm) REVERT: G 67 PHE cc_start: 0.8088 (m-80) cc_final: 0.7728 (m-80) REVERT: G 79 TYR cc_start: 0.8690 (m-10) cc_final: 0.8449 (m-80) REVERT: B 253 LEU cc_start: 0.9509 (mt) cc_final: 0.9276 (tt) REVERT: E 540 GLU cc_start: 0.7266 (tp30) cc_final: 0.6940 (tp30) REVERT: K 46 LYS cc_start: 0.9363 (ptmm) cc_final: 0.8883 (pptt) REVERT: K 47 LEU cc_start: 0.8723 (pp) cc_final: 0.8430 (pp) REVERT: I 82 MET cc_start: 0.9015 (mmm) cc_final: 0.8727 (mmm) REVERT: C 99 TYR cc_start: 0.8893 (p90) cc_final: 0.8361 (p90) REVERT: C 253 LEU cc_start: 0.9470 (mt) cc_final: 0.9198 (tt) REVERT: F 587 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8622 (ttp80) REVERT: F 591 ASP cc_start: 0.9136 (m-30) cc_final: 0.8529 (m-30) REVERT: F 615 TRP cc_start: 0.7570 (t-100) cc_final: 0.7125 (t-100) REVERT: L 46 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8914 (pptt) REVERT: L 47 LEU cc_start: 0.8820 (pp) cc_final: 0.8532 (pp) REVERT: L 48 LEU cc_start: 0.9348 (mt) cc_final: 0.8806 (mt) REVERT: J 79 TYR cc_start: 0.8530 (m-80) cc_final: 0.8258 (m-80) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.1408 time to fit residues: 34.0497 Evaluate side-chains 130 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 124 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN ** L 38 GLN ** 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 = 0.3138 r_free = 0.3138 target = 0.043616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035537 restraints weight = 113484.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036567 restraints weight = 71859.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037308 restraints weight = 51647.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.037756 restraints weight = 40511.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.038100 restraints weight = 34193.326| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13962 Z= 0.123 Angle : 0.669 9.249 19053 Z= 0.329 Chirality : 0.045 0.204 2166 Planarity : 0.005 0.075 2382 Dihedral : 6.109 81.523 1827 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.84 (0.21), residues: 1653 helix: 0.28 (0.35), residues: 210 sheet: -1.16 (0.23), residues: 519 loop : -1.61 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 97 TYR 0.022 0.001 TYR K 88 PHE 0.026 0.001 PHE J 100E TRP 0.031 0.001 TRP B 104 HIS 0.004 0.001 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13914) covalent geometry : angle 0.66109 / 0.33 (18930) SS BOND : bond 0.00215 / 0.15 ( 21) SS BOND : angle 0.50324 / 0.30 ( 42) hydrogen bonds : bond 0.03366 / 2.30 ( 387) hydrogen bonds : angle 5.85056 / 4.22 ( 999) link_ALPHA1-3 : bond 0.00680 / 0.31 ( 3) link_ALPHA1-3 : angle 1.38823 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00730 / 0.33 ( 3) link_ALPHA1-6 : angle 1.27217 / 0.68 ( 9) link_BETA1-4 : bond 0.00491 / 0.23 ( 9) link_BETA1-4 : angle 1.79372 / 0.99 ( 27) link_NAG-ASN : bond 0.00773 / 0.39 ( 12) link_NAG-ASN : angle 1.79844 / 1.18 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8680 (p90) cc_final: 0.8441 (p90) REVERT: A 130 ARG cc_start: 0.8730 (mpp80) cc_final: 0.8280 (mpp80) REVERT: A 163 ASP cc_start: 0.8583 (t70) cc_final: 0.8248 (t0) REVERT: A 253 LEU cc_start: 0.9482 (mt) cc_final: 0.9211 (tt) REVERT: D 587 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8498 (ttp80) REVERT: D 591 ASP cc_start: 0.9117 (m-30) cc_final: 0.8470 (m-30) REVERT: H 46 LYS cc_start: 0.9274 (ptmm) cc_final: 0.8745 (ptmm) REVERT: H 47 LEU cc_start: 0.8663 (pp) cc_final: 0.8456 (pp) REVERT: G 28 THR cc_start: 0.8805 (p) cc_final: 0.8442 (p) REVERT: G 32 TYR cc_start: 0.9025 (m-80) cc_final: 0.8454 (m-80) REVERT: G 67 PHE cc_start: 0.8027 (m-80) cc_final: 0.7769 (m-80) REVERT: G 79 TYR cc_start: 0.8707 (m-10) cc_final: 0.8452 (m-80) REVERT: G 82 MET cc_start: 0.8934 (mmp) cc_final: 0.8587 (mmp) REVERT: B 99 TYR cc_start: 0.8568 (p90) cc_final: 0.8104 (p90) REVERT: E 591 ASP cc_start: 0.9352 (m-30) cc_final: 0.8933 (m-30) REVERT: K 46 LYS cc_start: 0.9330 (ptmm) cc_final: 0.8801 (pptt) REVERT: K 47 LEU cc_start: 0.8727 (pp) cc_final: 0.8387 (pp) REVERT: I 82 MET cc_start: 0.9003 (mmm) cc_final: 0.8756 (mmm) REVERT: C 99 TYR cc_start: 0.8872 (p90) cc_final: 0.8334 (p90) REVERT: C 111 LEU cc_start: 0.9636 (mt) cc_final: 0.9426 (mt) REVERT: C 253 LEU cc_start: 0.9485 (mt) cc_final: 0.9173 (tt) REVERT: F 561 LEU cc_start: 0.9221 (tt) cc_final: 0.9017 (tt) REVERT: F 564 GLU cc_start: 0.8736 (mp0) cc_final: 0.8531 (mp0) REVERT: F 567 GLN cc_start: 0.9382 (tt0) cc_final: 0.9050 (tt0) REVERT: F 587 ARG cc_start: 0.9009 (mtp-110) cc_final: 0.8643 (ttp80) REVERT: F 591 ASP cc_start: 0.9178 (m-30) cc_final: 0.8579 (m-30) REVERT: F 615 TRP cc_start: 0.7479 (t-100) cc_final: 0.7182 (t-100) REVERT: L 46 LYS cc_start: 0.9211 (ptmm) cc_final: 0.8833 (pptt) REVERT: L 47 LEU cc_start: 0.8790 (pp) cc_final: 0.8458 (pp) REVERT: L 48 LEU cc_start: 0.9348 (mt) cc_final: 0.8838 (mt) REVERT: J 79 TYR cc_start: 0.8559 (m-80) cc_final: 0.8271 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1382 time to fit residues: 32.7171 Evaluate side-chains 133 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 38 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 521 GLN H 39 GLN ** L 38 GLN ** 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 = 0.3145 r_free = 0.3145 target = 0.043801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035674 restraints weight = 112813.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.036714 restraints weight = 70995.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.037461 restraints weight = 50859.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.037921 restraints weight = 39728.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.038339 restraints weight = 33796.115| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13962 Z= 0.112 Angle : 0.660 9.398 19053 Z= 0.323 Chirality : 0.045 0.200 2166 Planarity : 0.005 0.068 2382 Dihedral : 5.984 81.945 1827 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.14 % Allowed : 0.14 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.72 (0.21), residues: 1653 helix: 0.41 (0.35), residues: 210 sheet: -0.98 (0.24), residues: 486 loop : -1.60 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 587 TYR 0.020 0.001 TYR K 88 PHE 0.023 0.001 PHE J 100E TRP 0.019 0.001 TRP B 104 HIS 0.004 0.001 HIS E 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13914) covalent geometry : angle 0.65351 / 0.32 (18930) SS BOND : bond 0.00193 / 0.13 ( 21) SS BOND : angle 0.44972 / 0.27 ( 42) hydrogen bonds : bond 0.03237 / 2.20 ( 387) hydrogen bonds : angle 5.71195 / 4.12 ( 999) link_ALPHA1-3 : bond 0.00654 / 0.30 ( 3) link_ALPHA1-3 : angle 1.36537 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00705 / 0.33 ( 3) link_ALPHA1-6 : angle 1.26998 / 0.68 ( 9) link_BETA1-4 : bond 0.00525 / 0.23 ( 9) link_BETA1-4 : angle 1.60863 / 0.90 ( 27) link_NAG-ASN : bond 0.00750 / 0.37 ( 12) link_NAG-ASN : angle 1.77803 / 1.20 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.19 seconds wall clock time: 36 minutes 46.56 seconds (2206.56 seconds total)