Starting phenix.real_space_refine on Tue Nov 18 11:39:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_8936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_8936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_8936.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_8936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzm_8936/11_2025/6dzm_8936.cif" } 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-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 3 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 dihedrals: 3 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: 2.46, per 1000 atoms: 0.18 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: 1.25 Conformation dependent library (CDL) restraints added in 567.5 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: 0.35 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: 2.05 Time building geometry restraints manager: 1.56 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 - 23.20: 8222 23.20 - 46.39: 178 46.39 - 69.59: 51 69.59 - 92.79: 24 92.79 - 115.98: 12 Dihedral angle restraints: 8487 sinusoidal: 3642 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 8484 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.800 Find NCS groups from input model: 0.110 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 12.552 115.981 5328 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 covalent geometry : bond 0.00782 (13914) covalent geometry : angle 0.95646 (18930) SS BOND : bond 0.01136 ( 21) SS BOND : angle 7.07991 ( 42) hydrogen bonds : bond 0.23347 ( 387) hydrogen bonds : angle 10.40260 ( 999) link_ALPHA1-3 : bond 0.00466 ( 3) link_ALPHA1-3 : angle 1.86241 ( 9) link_ALPHA1-6 : bond 0.00515 ( 3) link_ALPHA1-6 : angle 1.67791 ( 9) link_BETA1-4 : bond 0.00439 ( 9) link_BETA1-4 : angle 5.46634 ( 27) link_NAG-ASN : bond 0.02158 ( 12) link_NAG-ASN : angle 4.35536 ( 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 : 0.432 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: 0.8979 (tt0) REVERT: F 588 LYS cc_start: 0.9110 (tppt) cc_final: 0.8805 (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: 0.1834 time to fit residues: 75.9165 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 : 0.390 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 224 ASN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN C 224 ASN F 595 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 = 0.3279 r_free = 0.3279 target = 0.047834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.039820 restraints weight = 112312.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.040925 restraints weight = 71211.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.041719 restraints weight = 50897.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.042256 restraints weight = 39403.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.042499 restraints weight = 32538.196| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13962 Z= 0.180 Angle : 0.838 12.482 19053 Z= 0.411 Chirality : 0.049 0.244 2166 Planarity : 0.007 0.084 2382 Dihedral : 12.330 80.478 2376 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.35 % Allowed : 1.40 % Favored : 98.25 % 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: -3.70 (0.19), residues: 1653 helix: -1.03 (0.33), residues: 213 sheet: -3.19 (0.18), residues: 453 loop : -2.48 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 54 TYR 0.019 0.002 TYR L 88 PHE 0.016 0.002 PHE J 67 TRP 0.031 0.002 TRP J 103 HIS 0.005 0.001 HIS J 100D Details of bonding type rmsd covalent geometry : bond 0.00388 (13914) covalent geometry : angle 0.80819 (18930) SS BOND : bond 0.00379 ( 21) SS BOND : angle 1.88725 ( 42) hydrogen bonds : bond 0.04892 ( 387) hydrogen bonds : angle 7.06914 ( 999) link_ALPHA1-3 : bond 0.01542 ( 3) link_ALPHA1-3 : angle 1.21157 ( 9) link_ALPHA1-6 : bond 0.00905 ( 3) link_ALPHA1-6 : angle 1.29408 ( 9) link_BETA1-4 : bond 0.00524 ( 9) link_BETA1-4 : angle 3.57190 ( 27) link_NAG-ASN : bond 0.01134 ( 12) link_NAG-ASN : angle 3.72462 ( 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 247 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 242 time to evaluate : 0.422 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 33 ILE cc_start: 0.8979 (mt) cc_final: 0.8669 (mm) REVERT: A 49 ASP cc_start: 0.8829 (p0) cc_final: 0.8451 (p0) REVERT: A 163 ASP cc_start: 0.8913 (t0) cc_final: 0.8690 (t0) REVERT: D 591 ASP cc_start: 0.8930 (m-30) cc_final: 0.8586 (m-30) REVERT: D 602 HIS cc_start: 0.8977 (m-70) cc_final: 0.8703 (t70) REVERT: H 87 TYR cc_start: 0.8603 (m-10) cc_final: 0.8257 (m-80) REVERT: G 32 TYR cc_start: 0.8933 (m-80) cc_final: 0.8219 (m-80) REVERT: B 33 ILE cc_start: 0.8978 (mt) cc_final: 0.8682 (mm) REVERT: B 49 ASP cc_start: 0.8749 (p0) cc_final: 0.8332 (p0) REVERT: B 163 ASP cc_start: 0.8937 (t0) cc_final: 0.8658 (t0) REVERT: E 584 ILE cc_start: 0.8921 (pt) cc_final: 0.8686 (mp) REVERT: E 587 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8688 (mtp-110) REVERT: E 591 ASP cc_start: 0.8894 (m-30) cc_final: 0.8559 (m-30) REVERT: E 602 HIS cc_start: 0.9064 (m-70) cc_final: 0.8802 (t70) REVERT: E 618 ASN cc_start: 0.7130 (p0) cc_final: 0.6029 (t0) REVERT: K 87 TYR cc_start: 0.8761 (m-80) cc_final: 0.8312 (m-10) REVERT: I 67 PHE cc_start: 0.8873 (m-80) cc_final: 0.8669 (m-80) REVERT: I 80 LEU cc_start: 0.9805 (tp) cc_final: 0.9242 (tp) REVERT: C 33 ILE cc_start: 0.8984 (mt) cc_final: 0.8606 (mt) REVERT: C 49 ASP cc_start: 0.9040 (p0) cc_final: 0.8540 (p0) REVERT: C 163 ASP cc_start: 0.8466 (t0) cc_final: 0.8239 (t0) REVERT: F 567 GLN cc_start: 0.9368 (tt0) cc_final: 0.9060 (tm-30) REVERT: F 571 LEU cc_start: 0.9281 (mt) cc_final: 0.8806 (mt) REVERT: F 584 ILE cc_start: 0.9162 (pt) cc_final: 0.8958 (mp) REVERT: F 587 ARG cc_start: 0.9018 (mtp-110) cc_final: 0.8708 (mtp-110) REVERT: F 591 ASP cc_start: 0.9020 (m-30) cc_final: 0.8633 (m-30) REVERT: F 602 HIS cc_start: 0.9133 (m-70) cc_final: 0.8809 (t70) REVERT: L 87 TYR cc_start: 0.8538 (m-10) cc_final: 0.8118 (m-10) REVERT: J 79 TYR cc_start: 0.8573 (m-80) cc_final: 0.8336 (m-80) outliers start: 5 outliers final: 0 residues processed: 246 average time/residue: 0.1370 time to fit residues: 45.5582 Evaluate side-chains 136 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 0.0010 chunk 7 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 560 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036362 restraints weight = 116124.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037387 restraints weight = 72856.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038147 restraints weight = 52511.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.038596 restraints weight = 40828.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.039036 restraints weight = 34618.160| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13962 Z= 0.241 Angle : 0.809 10.143 19053 Z= 0.398 Chirality : 0.049 0.297 2166 Planarity : 0.007 0.109 2382 Dihedral : 10.722 77.984 2376 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.21 % Allowed : 2.87 % Favored : 96.92 % 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: -0.37 (0.34), residues: 213 sheet: -2.75 (0.19), residues: 447 loop : -2.23 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 38 TYR 0.019 0.002 TYR K 88 PHE 0.015 0.002 PHE G 100E TRP 0.029 0.002 TRP C 86 HIS 0.006 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00512 (13914) covalent geometry : angle 0.78511 (18930) SS BOND : bond 0.00341 ( 21) SS BOND : angle 0.99617 ( 42) hydrogen bonds : bond 0.04290 ( 387) hydrogen bonds : angle 6.51777 ( 999) link_ALPHA1-3 : bond 0.00602 ( 3) link_ALPHA1-3 : angle 1.76045 ( 9) link_ALPHA1-6 : bond 0.01150 ( 3) link_ALPHA1-6 : angle 1.94524 ( 9) link_BETA1-4 : bond 0.00474 ( 9) link_BETA1-4 : angle 3.63774 ( 27) link_NAG-ASN : bond 0.00962 ( 12) link_NAG-ASN : angle 3.05681 ( 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 186 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.455 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: D 587 ARG cc_start: 0.9101 (mtp-110) cc_final: 0.8418 (ttp80) REVERT: D 591 ASP cc_start: 0.9190 (m-30) cc_final: 0.8544 (m-30) REVERT: G 32 TYR cc_start: 0.8801 (m-80) cc_final: 0.8277 (m-80) REVERT: G 45 LEU cc_start: 0.9078 (mm) cc_final: 0.8694 (mm) REVERT: B 86 TRP cc_start: 0.9060 (m-10) cc_final: 0.8256 (m-90) REVERT: B 163 ASP cc_start: 0.9007 (t0) cc_final: 0.8749 (t0) REVERT: E 584 ILE cc_start: 0.9229 (pt) cc_final: 0.8988 (mp) REVERT: E 587 ARG cc_start: 0.9018 (mtp-110) cc_final: 0.8414 (ttp80) REVERT: E 591 ASP cc_start: 0.9199 (m-30) cc_final: 0.8121 (m-30) REVERT: C 49 ASP cc_start: 0.8390 (p0) cc_final: 0.8184 (p0) REVERT: F 587 ARG cc_start: 0.9107 (mtp-110) cc_final: 0.8869 (mtp-110) REVERT: F 591 ASP cc_start: 0.9135 (m-30) cc_final: 0.8678 (m-30) REVERT: F 595 GLN cc_start: 0.9479 (pt0) cc_final: 0.9155 (pp30) REVERT: F 602 HIS cc_start: 0.9232 (m-70) cc_final: 0.8797 (t70) REVERT: J 79 TYR cc_start: 0.8550 (m-80) cc_final: 0.8151 (m-80) outliers start: 3 outliers final: 0 residues processed: 186 average time/residue: 0.1452 time to fit residues: 37.0508 Evaluate side-chains 115 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.040914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.033190 restraints weight = 116076.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034111 restraints weight = 75330.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.034776 restraints weight = 55154.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035225 restraints weight = 43870.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.035434 restraints weight = 37236.434| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13962 Z= 0.380 Angle : 0.946 8.754 19053 Z= 0.470 Chirality : 0.052 0.260 2166 Planarity : 0.009 0.178 2382 Dihedral : 10.293 75.225 2376 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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: -3.02 (0.20), residues: 1653 helix: -0.62 (0.31), residues: 213 sheet: -2.38 (0.20), residues: 495 loop : -2.14 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG A 134 TYR 0.031 0.003 TYR K 87 PHE 0.036 0.003 PHE J 67 TRP 0.028 0.003 TRP B 275 HIS 0.010 0.002 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00806 (13914) covalent geometry : angle 0.92397 (18930) SS BOND : bond 0.00470 ( 21) SS BOND : angle 0.92999 ( 42) hydrogen bonds : bond 0.04545 ( 387) hydrogen bonds : angle 6.64645 ( 999) link_ALPHA1-3 : bond 0.00782 ( 3) link_ALPHA1-3 : angle 1.86598 ( 9) link_ALPHA1-6 : bond 0.00907 ( 3) link_ALPHA1-6 : angle 1.81722 ( 9) link_BETA1-4 : bond 0.00368 ( 9) link_BETA1-4 : angle 3.99690 ( 27) link_NAG-ASN : bond 0.00925 ( 12) link_NAG-ASN : angle 3.16666 ( 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 159 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.368 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 591 ASP cc_start: 0.9297 (m-30) cc_final: 0.8918 (m-30) REVERT: H 39 GLN cc_start: 0.9083 (pt0) cc_final: 0.8762 (pp30) REVERT: G 32 TYR cc_start: 0.9103 (m-80) cc_final: 0.8524 (m-80) REVERT: B 163 ASP cc_start: 0.9030 (t0) cc_final: 0.8829 (t0) REVERT: E 591 ASP cc_start: 0.9356 (m-30) cc_final: 0.9006 (m-30) REVERT: I 34 MET cc_start: 0.8744 (mmt) cc_final: 0.8502 (mmm) REVERT: C 47 ASP cc_start: 0.8589 (t0) cc_final: 0.8312 (t0) REVERT: C 49 ASP cc_start: 0.8144 (p0) cc_final: 0.7939 (p0) REVERT: C 99 TYR cc_start: 0.9270 (p90) cc_final: 0.8704 (p90) REVERT: F 591 ASP cc_start: 0.9303 (m-30) cc_final: 0.8926 (m-30) REVERT: F 615 TRP cc_start: 0.7314 (t-100) cc_final: 0.6504 (t-100) REVERT: J 34 MET cc_start: 0.8655 (mmt) cc_final: 0.8307 (mpp) REVERT: J 82 MET cc_start: 0.9079 (mmp) cc_final: 0.8863 (mmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1351 time to fit residues: 29.4831 Evaluate side-chains 111 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.7980 chunk 164 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN E 570 GLN E 602 HIS K 38 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN L 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034890 restraints weight = 111257.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035913 restraints weight = 70616.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036645 restraints weight = 50831.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037072 restraints weight = 39830.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.037468 restraints weight = 33625.191| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13962 Z= 0.141 Angle : 0.729 9.220 19053 Z= 0.356 Chirality : 0.048 0.233 2166 Planarity : 0.006 0.071 2382 Dihedral : 9.495 80.005 2376 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.14 % Allowed : 2.45 % Favored : 97.41 % 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: -2.54 (0.20), residues: 1653 helix: -0.08 (0.33), residues: 213 sheet: -1.81 (0.23), residues: 432 loop : -2.05 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.028 0.002 TYR B 162 PHE 0.019 0.002 PHE I 67 TRP 0.017 0.002 TRP D 615 HIS 0.003 0.001 HIS E 613 Details of bonding type rmsd covalent geometry : bond 0.00309 (13914) covalent geometry : angle 0.70888 (18930) SS BOND : bond 0.00274 ( 21) SS BOND : angle 0.53050 ( 42) hydrogen bonds : bond 0.03739 ( 387) hydrogen bonds : angle 6.11858 ( 999) link_ALPHA1-3 : bond 0.01296 ( 3) link_ALPHA1-3 : angle 0.92628 ( 9) link_ALPHA1-6 : bond 0.00827 ( 3) link_ALPHA1-6 : angle 1.86450 ( 9) link_BETA1-4 : bond 0.00554 ( 9) link_BETA1-4 : angle 3.49414 ( 27) link_NAG-ASN : bond 0.00969 ( 12) link_NAG-ASN : angle 2.58467 ( 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 181 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 179 time to evaluate : 0.524 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: 0.9609 (mt) cc_final: 0.9306 (tt) REVERT: D 587 ARG cc_start: 0.9072 (mtp-110) cc_final: 0.8464 (ttp80) REVERT: D 591 ASP cc_start: 0.9322 (m-30) cc_final: 0.8677 (m-30) REVERT: H 39 GLN cc_start: 0.8923 (pt0) cc_final: 0.8631 (pp30) REVERT: G 32 TYR cc_start: 0.9039 (m-80) cc_final: 0.8800 (m-80) REVERT: B 163 ASP cc_start: 0.9057 (t0) cc_final: 0.8799 (t0) REVERT: B 253 LEU cc_start: 0.9512 (mt) cc_final: 0.9224 (tt) REVERT: E 591 ASP cc_start: 0.9359 (m-30) cc_final: 0.8991 (m-30) REVERT: E 618 ASN cc_start: 0.7666 (p0) cc_final: 0.7371 (p0) REVERT: I 34 MET cc_start: 0.8700 (mmt) cc_final: 0.8493 (mmm) REVERT: I 45 LEU cc_start: 0.9014 (mm) cc_final: 0.8800 (mm) REVERT: I 80 LEU cc_start: 0.9738 (tp) cc_final: 0.9328 (tp) REVERT: C 49 ASP cc_start: 0.8129 (p0) cc_final: 0.7866 (p0) REVERT: C 99 TYR cc_start: 0.8873 (p90) cc_final: 0.8517 (p90) REVERT: C 130 ARG cc_start: 0.8816 (mpp80) cc_final: 0.8521 (mpp80) REVERT: C 253 LEU cc_start: 0.9455 (mt) cc_final: 0.9128 (tt) REVERT: F 567 GLN cc_start: 0.9350 (tt0) cc_final: 0.8907 (tt0) REVERT: F 587 ARG cc_start: 0.9130 (mtp-110) cc_final: 0.8378 (ttp80) REVERT: F 591 ASP cc_start: 0.9285 (m-30) cc_final: 0.8561 (m-30) REVERT: F 615 TRP cc_start: 0.7589 (t-100) cc_final: 0.7244 (t-100) REVERT: J 34 MET cc_start: 0.8682 (mmt) cc_final: 0.8467 (mmm) REVERT: J 45 LEU cc_start: 0.8877 (mm) cc_final: 0.8643 (mm) REVERT: J 67 PHE cc_start: 0.8142 (m-80) cc_final: 0.7856 (m-10) REVERT: J 79 TYR cc_start: 0.8416 (m-80) cc_final: 0.7969 (m-80) outliers start: 2 outliers final: 1 residues processed: 181 average time/residue: 0.1503 time to fit residues: 37.0004 Evaluate side-chains 128 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.033684 restraints weight = 114202.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.034648 restraints weight = 72523.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.035346 restraints weight = 52296.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035802 restraints weight = 41226.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.036096 restraints weight = 34732.496| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13962 Z= 0.231 Angle : 0.771 12.506 19053 Z= 0.378 Chirality : 0.052 0.880 2166 Planarity : 0.007 0.178 2382 Dihedral : 9.240 79.020 2376 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: 0.01 (0.33), residues: 213 sheet: -1.85 (0.22), residues: 480 loop : -1.92 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 134 TYR 0.029 0.002 TYR L 88 PHE 0.014 0.002 PHE E 572 TRP 0.015 0.002 TRP B 275 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00494 (13914) covalent geometry : angle 0.74880 (18930) SS BOND : bond 0.00246 ( 21) SS BOND : angle 0.60594 ( 42) hydrogen bonds : bond 0.03802 ( 387) hydrogen bonds : angle 6.16108 ( 999) link_ALPHA1-3 : bond 0.01122 ( 3) link_ALPHA1-3 : angle 1.33511 ( 9) link_ALPHA1-6 : bond 0.00875 ( 3) link_ALPHA1-6 : angle 1.67290 ( 9) link_BETA1-4 : bond 0.00302 ( 9) link_BETA1-4 : angle 3.65587 ( 27) link_NAG-ASN : bond 0.00800 ( 12) link_NAG-ASN : angle 2.87675 ( 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 154 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.515 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: A 99 TYR cc_start: 0.8888 (p90) cc_final: 0.8327 (p90) REVERT: A 253 LEU cc_start: 0.9601 (mt) cc_final: 0.9280 (tt) REVERT: D 521 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8647 (tm-30) REVERT: H 39 GLN cc_start: 0.9209 (pt0) cc_final: 0.8851 (tt0) REVERT: G 32 TYR cc_start: 0.9084 (m-80) cc_final: 0.8788 (m-80) REVERT: G 67 PHE cc_start: 0.8388 (m-80) cc_final: 0.8140 (m-10) REVERT: B 253 LEU cc_start: 0.9525 (mt) cc_final: 0.9222 (tt) REVERT: E 540 GLU cc_start: 0.7952 (tp30) cc_final: 0.7679 (tp30) REVERT: E 591 ASP cc_start: 0.9370 (m-30) cc_final: 0.9051 (m-30) REVERT: E 618 ASN cc_start: 0.7661 (p0) cc_final: 0.7401 (p0) REVERT: I 32 TYR cc_start: 0.8885 (m-80) cc_final: 0.8571 (m-80) REVERT: I 34 MET cc_start: 0.8756 (mmt) cc_final: 0.8517 (mmm) REVERT: I 45 LEU cc_start: 0.9154 (mm) cc_final: 0.8825 (mm) REVERT: C 99 TYR cc_start: 0.9089 (p90) cc_final: 0.8396 (p90) REVERT: C 253 LEU cc_start: 0.9448 (mt) cc_final: 0.9088 (tt) REVERT: F 567 GLN cc_start: 0.9331 (tt0) cc_final: 0.8872 (tt0) REVERT: F 591 ASP cc_start: 0.9304 (m-30) cc_final: 0.8934 (m-30) REVERT: J 34 MET cc_start: 0.8689 (mmt) cc_final: 0.8434 (mmm) REVERT: J 67 PHE cc_start: 0.8384 (m-80) cc_final: 0.8027 (m-80) REVERT: J 79 TYR cc_start: 0.8464 (m-80) cc_final: 0.8098 (m-80) REVERT: J 82 MET cc_start: 0.9194 (mmp) cc_final: 0.8428 (mmp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1451 time to fit residues: 30.8144 Evaluate side-chains 110 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN K 38 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3063 r_free = 0.3063 target = 0.041205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.033368 restraints weight = 112954.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.034350 restraints weight = 71764.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034892 restraints weight = 51774.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.035451 restraints weight = 42360.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.035745 restraints weight = 35363.798| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13962 Z= 0.225 Angle : 0.752 9.095 19053 Z= 0.373 Chirality : 0.049 0.490 2166 Planarity : 0.006 0.128 2382 Dihedral : 8.817 78.903 2376 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % 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: -2.34 (0.21), residues: 1653 helix: -0.06 (0.32), residues: 213 sheet: -1.65 (0.23), residues: 474 loop : -1.88 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 97 TYR 0.026 0.002 TYR H 88 PHE 0.033 0.002 PHE J 100E TRP 0.024 0.002 TRP D 615 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00484 (13914) covalent geometry : angle 0.73327 (18930) SS BOND : bond 0.00228 ( 21) SS BOND : angle 0.55542 ( 42) hydrogen bonds : bond 0.03844 ( 387) hydrogen bonds : angle 6.16878 ( 999) link_ALPHA1-3 : bond 0.01187 ( 3) link_ALPHA1-3 : angle 1.28965 ( 9) link_ALPHA1-6 : bond 0.00909 ( 3) link_ALPHA1-6 : angle 1.75828 ( 9) link_BETA1-4 : bond 0.00383 ( 9) link_BETA1-4 : angle 3.55786 ( 27) link_NAG-ASN : bond 0.00693 ( 12) link_NAG-ASN : angle 2.40403 ( 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 156 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.480 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: A 99 TYR cc_start: 0.8788 (p90) cc_final: 0.8209 (p90) REVERT: A 130 ARG cc_start: 0.9328 (mpp80) cc_final: 0.9114 (mpp80) REVERT: A 185 ILE cc_start: 0.9356 (mt) cc_final: 0.9062 (tp) REVERT: A 253 LEU cc_start: 0.9584 (mt) cc_final: 0.9260 (tt) REVERT: D 521 GLN cc_start: 0.9035 (tm130) cc_final: 0.8729 (tm-30) REVERT: D 561 LEU cc_start: 0.9311 (tt) cc_final: 0.8950 (tt) REVERT: G 32 TYR cc_start: 0.9055 (m-80) cc_final: 0.8727 (m-80) REVERT: G 45 LEU cc_start: 0.9122 (mm) cc_final: 0.8794 (mm) REVERT: G 79 TYR cc_start: 0.8819 (m-80) cc_final: 0.8591 (m-10) REVERT: B 163 ASP cc_start: 0.8873 (t70) cc_final: 0.8430 (t0) REVERT: B 253 LEU cc_start: 0.9514 (mt) cc_final: 0.9230 (tt) REVERT: E 540 GLU cc_start: 0.7925 (tp30) cc_final: 0.7663 (tp30) REVERT: E 587 ARG cc_start: 0.9258 (mtp-110) cc_final: 0.8912 (ttp80) REVERT: I 32 TYR cc_start: 0.8923 (m-80) cc_final: 0.8581 (m-80) REVERT: I 34 MET cc_start: 0.8738 (mmt) cc_final: 0.8519 (mmm) REVERT: I 45 LEU cc_start: 0.9165 (mm) cc_final: 0.8904 (mm) REVERT: C 99 TYR cc_start: 0.9118 (p90) cc_final: 0.8460 (p90) REVERT: C 253 LEU cc_start: 0.9432 (mt) cc_final: 0.9091 (tt) REVERT: F 567 GLN cc_start: 0.9342 (tt0) cc_final: 0.8901 (tt0) REVERT: F 587 ARG cc_start: 0.9060 (mtp-110) cc_final: 0.8492 (ttp80) REVERT: F 591 ASP cc_start: 0.9351 (m-30) cc_final: 0.8824 (m-30) REVERT: F 615 TRP cc_start: 0.7661 (t-100) cc_final: 0.7065 (t-100) REVERT: L 46 LYS cc_start: 0.9231 (ptmm) cc_final: 0.8901 (pptt) REVERT: J 79 TYR cc_start: 0.8549 (m-80) cc_final: 0.8086 (m-80) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1467 time to fit residues: 31.4513 Evaluate side-chains 117 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.0970 chunk 47 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3094 r_free = 0.3094 target = 0.042362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.034508 restraints weight = 112063.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.035528 restraints weight = 70102.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.036229 restraints weight = 50052.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.036710 restraints weight = 39131.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.037111 restraints weight = 32682.997| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13962 Z= 0.130 Angle : 0.720 9.375 19053 Z= 0.355 Chirality : 0.049 0.732 2166 Planarity : 0.005 0.075 2382 Dihedral : 8.346 81.327 2376 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -2.07 (0.21), residues: 1653 helix: -0.15 (0.32), residues: 210 sheet: -1.20 (0.24), residues: 474 loop : -1.78 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 97 TYR 0.024 0.001 TYR H 88 PHE 0.024 0.002 PHE I 100E TRP 0.013 0.001 TRP F 518 HIS 0.004 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00283 (13914) covalent geometry : angle 0.70002 (18930) SS BOND : bond 0.00210 ( 21) SS BOND : angle 0.44857 ( 42) hydrogen bonds : bond 0.03774 ( 387) hydrogen bonds : angle 6.07907 ( 999) link_ALPHA1-3 : bond 0.01289 ( 3) link_ALPHA1-3 : angle 1.15218 ( 9) link_ALPHA1-6 : bond 0.00916 ( 3) link_ALPHA1-6 : angle 1.73010 ( 9) link_BETA1-4 : bond 0.00535 ( 9) link_BETA1-4 : angle 3.29398 ( 27) link_NAG-ASN : bond 0.00883 ( 12) link_NAG-ASN : angle 2.64658 ( 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 173 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.546 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: D 561 LEU cc_start: 0.9255 (tt) cc_final: 0.8975 (tt) REVERT: D 564 GLU cc_start: 0.8663 (mp0) cc_final: 0.8449 (mp0) REVERT: G 32 TYR cc_start: 0.8999 (m-80) cc_final: 0.8650 (m-80) REVERT: G 45 LEU cc_start: 0.9086 (mm) cc_final: 0.8638 (mm) REVERT: G 79 TYR cc_start: 0.8749 (m-80) cc_final: 0.8540 (m-10) REVERT: G 82 MET cc_start: 0.9122 (mmp) cc_final: 0.8838 (mmp) REVERT: B 163 ASP cc_start: 0.8724 (t70) cc_final: 0.8296 (t0) REVERT: E 540 GLU cc_start: 0.7899 (tp30) cc_final: 0.7630 (tp30) REVERT: E 587 ARG cc_start: 0.9190 (mtp-110) cc_final: 0.8576 (ttp80) REVERT: K 46 LYS cc_start: 0.9305 (ptmm) cc_final: 0.8905 (pptt) REVERT: K 48 LEU cc_start: 0.9341 (mt) cc_final: 0.8996 (mt) REVERT: I 32 TYR cc_start: 0.8785 (m-80) cc_final: 0.8551 (m-80) REVERT: I 45 LEU cc_start: 0.9079 (mm) cc_final: 0.8855 (mm) REVERT: C 99 TYR cc_start: 0.8880 (p90) cc_final: 0.8290 (p90) REVERT: C 253 LEU cc_start: 0.9430 (mt) cc_final: 0.9089 (tt) REVERT: F 561 LEU cc_start: 0.9390 (tt) cc_final: 0.9137 (tt) REVERT: F 564 GLU cc_start: 0.8685 (mp0) cc_final: 0.8454 (mp0) REVERT: F 567 GLN cc_start: 0.9316 (tt0) cc_final: 0.8897 (tt0) REVERT: F 587 ARG cc_start: 0.9010 (mtp-110) cc_final: 0.8462 (ttp80) REVERT: F 591 ASP cc_start: 0.9248 (m-30) cc_final: 0.8586 (m-30) REVERT: L 46 LYS cc_start: 0.9204 (ptmm) cc_final: 0.8921 (pptt) REVERT: L 48 LEU cc_start: 0.9291 (mt) cc_final: 0.8818 (mt) REVERT: J 79 TYR cc_start: 0.8447 (m-80) cc_final: 0.8069 (m-80) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1421 time to fit residues: 34.1207 Evaluate side-chains 118 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN ** D 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3059 r_free = 0.3059 target = 0.040956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.033234 restraints weight = 115554.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.034218 restraints weight = 72598.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.034929 restraints weight = 52091.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035341 restraints weight = 40785.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035723 restraints weight = 34485.572| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13962 Z= 0.231 Angle : 0.774 9.219 19053 Z= 0.384 Chirality : 0.049 0.651 2166 Planarity : 0.006 0.080 2382 Dihedral : 8.239 78.113 2376 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.14 % Allowed : 0.91 % Favored : 98.95 % 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: -2.20 (0.21), residues: 1653 helix: -0.42 (0.32), residues: 210 sheet: -1.46 (0.23), residues: 513 loop : -1.70 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 97 TYR 0.027 0.002 TYR H 88 PHE 0.027 0.002 PHE I 100E TRP 0.026 0.002 TRP F 615 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00496 (13914) covalent geometry : angle 0.75504 (18930) SS BOND : bond 0.00215 ( 21) SS BOND : angle 0.54167 ( 42) hydrogen bonds : bond 0.03946 ( 387) hydrogen bonds : angle 6.23794 ( 999) link_ALPHA1-3 : bond 0.00898 ( 3) link_ALPHA1-3 : angle 1.47616 ( 9) link_ALPHA1-6 : bond 0.00843 ( 3) link_ALPHA1-6 : angle 1.62749 ( 9) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 3.33347 ( 27) link_NAG-ASN : bond 0.00709 ( 12) link_NAG-ASN : angle 2.72751 ( 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 151 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.494 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: G 32 TYR cc_start: 0.9089 (m-80) cc_final: 0.8747 (m-80) REVERT: G 79 TYR cc_start: 0.8749 (m-80) cc_final: 0.8536 (m-10) REVERT: B 163 ASP cc_start: 0.8842 (t70) cc_final: 0.8450 (t0) REVERT: B 229 MET cc_start: 0.8785 (ppp) cc_final: 0.8488 (ppp) REVERT: E 540 GLU cc_start: 0.8018 (tp30) cc_final: 0.7737 (tp30) REVERT: K 46 LYS cc_start: 0.9390 (ptmm) cc_final: 0.8880 (pptt) REVERT: K 47 LEU cc_start: 0.8965 (pp) cc_final: 0.8694 (pp) REVERT: C 99 TYR cc_start: 0.9158 (p90) cc_final: 0.8411 (p90) REVERT: C 253 LEU cc_start: 0.9467 (mt) cc_final: 0.9201 (tt) REVERT: F 564 GLU cc_start: 0.8642 (mp0) cc_final: 0.8328 (mp0) REVERT: F 567 GLN cc_start: 0.9357 (tt0) cc_final: 0.8929 (tt0) REVERT: F 587 ARG cc_start: 0.9115 (mtp-110) cc_final: 0.8455 (ttp80) REVERT: F 591 ASP cc_start: 0.9396 (m-30) cc_final: 0.8854 (m-30) REVERT: L 46 LYS cc_start: 0.9267 (ptmm) cc_final: 0.8867 (pptt) REVERT: L 47 LEU cc_start: 0.8902 (pp) cc_final: 0.8669 (pp) REVERT: J 79 TYR cc_start: 0.8609 (m-80) cc_final: 0.8116 (m-80) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1500 time to fit residues: 30.9276 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 : 0.483 ------------------------------------------------------------------------------- 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: 0.6980 chunk 114 optimal weight: 0.1980 chunk 116 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN D 551 GLN K 38 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.042420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034600 restraints weight = 112716.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.035634 restraints weight = 70900.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036367 restraints weight = 50769.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.036823 restraints weight = 39577.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037177 restraints weight = 33234.695| |-----------------------------------------------------------------------------| r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 13962 Z= 0.131 Angle : 0.734 9.364 19053 Z= 0.364 Chirality : 0.048 0.509 2166 Planarity : 0.005 0.054 2382 Dihedral : 7.904 80.444 2376 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.28 % Allowed : 0.21 % Favored : 99.51 % 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: -2.01 (0.21), residues: 1653 helix: -0.21 (0.33), residues: 210 sheet: -1.19 (0.23), residues: 480 loop : -1.69 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 134 TYR 0.024 0.001 TYR H 88 PHE 0.015 0.002 PHE F 535 TRP 0.060 0.002 TRP F 615 HIS 0.009 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00290 (13914) covalent geometry : angle 0.71615 (18930) SS BOND : bond 0.00270 ( 21) SS BOND : angle 0.54546 ( 42) hydrogen bonds : bond 0.03760 ( 387) hydrogen bonds : angle 6.01806 ( 999) link_ALPHA1-3 : bond 0.01195 ( 3) link_ALPHA1-3 : angle 1.22321 ( 9) link_ALPHA1-6 : bond 0.00940 ( 3) link_ALPHA1-6 : angle 1.65183 ( 9) link_BETA1-4 : bond 0.00529 ( 9) link_BETA1-4 : angle 3.08885 ( 27) link_NAG-ASN : bond 0.01079 ( 12) link_NAG-ASN : angle 2.59231 ( 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 167 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.547 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: G 32 TYR cc_start: 0.8990 (m-80) cc_final: 0.8613 (m-80) REVERT: E 540 GLU cc_start: 0.8048 (tp30) cc_final: 0.7794 (tp30) REVERT: E 587 ARG cc_start: 0.8608 (ttp80) cc_final: 0.7936 (ttp80) REVERT: K 46 LYS cc_start: 0.9332 (ptmm) cc_final: 0.8784 (pptt) REVERT: K 47 LEU cc_start: 0.8737 (pp) cc_final: 0.8534 (pp) REVERT: K 48 LEU cc_start: 0.9342 (mt) cc_final: 0.9019 (mt) REVERT: C 99 TYR cc_start: 0.8849 (p90) cc_final: 0.8216 (p90) REVERT: C 253 LEU cc_start: 0.9466 (mt) cc_final: 0.9168 (tt) REVERT: F 561 LEU cc_start: 0.9399 (tt) cc_final: 0.9094 (tt) REVERT: F 564 GLU cc_start: 0.8693 (mp0) cc_final: 0.8339 (mp0) REVERT: F 567 GLN cc_start: 0.9342 (tt0) cc_final: 0.8960 (tt0) REVERT: F 587 ARG cc_start: 0.9089 (mtp-110) cc_final: 0.8538 (ttp80) REVERT: F 591 ASP cc_start: 0.9288 (m-30) cc_final: 0.8668 (m-30) REVERT: L 46 LYS cc_start: 0.9236 (ptmm) cc_final: 0.8816 (pptt) REVERT: L 48 LEU cc_start: 0.9380 (mt) cc_final: 0.9007 (mp) REVERT: J 79 TYR cc_start: 0.8523 (m-80) cc_final: 0.8291 (m-80) REVERT: J 103 TRP cc_start: 0.8787 (m100) cc_final: 0.8481 (m100) outliers start: 4 outliers final: 1 residues processed: 167 average time/residue: 0.1356 time to fit residues: 31.8475 Evaluate side-chains 119 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.9980 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.0170 chunk 38 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 0.0770 chunk 4 optimal weight: 0.0370 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN K 38 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.042751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.034842 restraints weight = 111207.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.035894 restraints weight = 68921.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036637 restraints weight = 49171.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037172 restraints weight = 38269.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.037497 restraints weight = 31912.505| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.6529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13962 Z= 0.121 Angle : 0.709 9.468 19053 Z= 0.350 Chirality : 0.047 0.441 2166 Planarity : 0.005 0.117 2382 Dihedral : 7.700 81.636 2376 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 0.14 % Allowed : 0.35 % Favored : 99.51 % 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: -1.80 (0.21), residues: 1653 helix: -0.15 (0.33), residues: 207 sheet: -0.99 (0.23), residues: 513 loop : -1.55 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 134 TYR 0.023 0.001 TYR L 88 PHE 0.026 0.002 PHE I 67 TRP 0.022 0.001 TRP F 615 HIS 0.007 0.001 HIS F 602 Details of bonding type rmsd covalent geometry : bond 0.00263 (13914) covalent geometry : angle 0.69305 (18930) SS BOND : bond 0.00234 ( 21) SS BOND : angle 0.55957 ( 42) hydrogen bonds : bond 0.03717 ( 387) hydrogen bonds : angle 5.93886 ( 999) link_ALPHA1-3 : bond 0.01025 ( 3) link_ALPHA1-3 : angle 1.26749 ( 9) link_ALPHA1-6 : bond 0.00889 ( 3) link_ALPHA1-6 : angle 1.55954 ( 9) link_BETA1-4 : bond 0.00510 ( 9) link_BETA1-4 : angle 2.98486 ( 27) link_NAG-ASN : bond 0.00999 ( 12) link_NAG-ASN : angle 2.35951 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.14 seconds wall clock time: 35 minutes 16.89 seconds (2116.89 seconds total)