Starting phenix.real_space_refine on Thu Sep 26 18:34:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_8936.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_8936.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_8936.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_8936.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dzm_8936/09_2024/6dzm_8936.cif" } resolution = 4.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: "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: "E" 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: "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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D, F, I, J, O, Q, P, R, K, L Time building chain proxies: 7.14, per 1000 atoms: 0.53 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=2, symmetry=0 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 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: 3.77 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.69 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: 3.98 Time building geometry restraints manager: 4.36 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: 8187 23.20 - 46.39: 164 46.39 - 69.59: 43 69.59 - 92.79: 24 92.79 - 115.98: 12 Dihedral angle restraints: 8430 sinusoidal: 3585 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 8427 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: 2.01 - 2.59: 244 2.59 - 3.16: 12310 3.16 - 3.74: 21055 3.74 - 4.32: 29663 4.32 - 4.90: 47127 Nonbonded interactions: 110399 Sorted by model distance: nonbonded pdb=" SG CYS A 53 " pdb=" SG CYS D 609 " model vdw 2.007 3.760 nonbonded pdb=" SG CYS B 53 " pdb=" SG CYS E 609 " model vdw 2.008 3.760 nonbonded pdb=" SG CYS C 53 " pdb=" SG CYS F 609 " model vdw 2.008 3.760 nonbonded pdb=" SG CYS E 601 " pdb=" SG CYS E 608 " model vdw 2.016 3.760 nonbonded pdb=" SG CYS F 601 " pdb=" SG CYS F 608 " model vdw 2.016 3.760 ... (remaining 110394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.460 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- 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 13914 Z= 0.510 Angle : 0.956 7.197 18930 Z= 0.494 Chirality : 0.054 0.237 2166 Planarity : 0.006 0.049 2382 Dihedral : 12.552 115.981 5328 Min Nonbonded Distance : 2.007 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.021 0.003 TRP F 597 HIS 0.009 0.003 HIS F 516 PHE 0.027 0.003 PHE A 160 TYR 0.025 0.002 TYR L 92 ARG 0.009 0.001 ARG C 85 *********************** 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 fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.640 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: A 33 ILE cc_start: 0.8833 (mt) cc_final: 0.8317 (mm) REVERT: A 39 HIS cc_start: 0.8481 (t70) cc_final: 0.8189 (t70) REVERT: A 163 ASP cc_start: 0.8933 (t0) cc_final: 0.7782 (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: 0.8731 (tttm) REVERT: D 591 ASP cc_start: 0.8806 (m-30) cc_final: 0.8499 (m-30) REVERT: H 87 TYR cc_start: 0.8474 (m-10) cc_final: 0.8196 (m-10) REVERT: H 103 LYS cc_start: 0.9478 (tptm) cc_final: 0.9223 (tppt) REVERT: G 32 TYR cc_start: 0.8878 (m-80) cc_final: 0.7951 (m-80) REVERT: B 33 ILE cc_start: 0.8871 (mt) cc_final: 0.8325 (mm) REVERT: B 162 TYR cc_start: 0.8707 (m-80) cc_final: 0.8487 (m-10) REVERT: B 163 ASP cc_start: 0.8864 (t0) cc_final: 0.8005 (t0) REVERT: E 588 LYS cc_start: 0.9165 (tppt) cc_final: 0.8942 (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: 0.8646 (m-30) REVERT: L 87 TYR cc_start: 0.8412 (m-10) cc_final: 0.8194 (m-10) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.3904 time to fit residues: 162.4128 Evaluate side-chains 144 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13914 Z= 0.240 Angle : 0.809 13.458 18930 Z= 0.403 Chirality : 0.049 0.244 2166 Planarity : 0.007 0.059 2382 Dihedral : 12.436 80.645 2376 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 0.28 % Allowed : 1.54 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.19), residues: 1653 helix: -1.09 (0.33), residues: 213 sheet: -3.17 (0.18), residues: 468 loop : -2.39 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP J 103 HIS 0.005 0.001 HIS J 100D PHE 0.019 0.002 PHE J 67 TYR 0.021 0.002 TYR G 79 ARG 0.012 0.001 ARG J 66 *********************** 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 245 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 1.418 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: A 33 ILE cc_start: 0.8950 (mt) cc_final: 0.8632 (mm) REVERT: A 49 ASP cc_start: 0.8804 (p0) cc_final: 0.8414 (p0) REVERT: A 163 ASP cc_start: 0.9146 (t0) cc_final: 0.8840 (t0) REVERT: D 591 ASP cc_start: 0.8894 (m-30) cc_final: 0.8523 (m-30) REVERT: H 87 TYR cc_start: 0.8299 (m-10) cc_final: 0.7942 (m-80) REVERT: G 32 TYR cc_start: 0.8906 (m-80) cc_final: 0.8226 (m-80) REVERT: B 33 ILE cc_start: 0.8914 (mt) cc_final: 0.8597 (mm) REVERT: B 49 ASP cc_start: 0.8750 (p0) cc_final: 0.8326 (p0) REVERT: B 163 ASP cc_start: 0.9110 (t0) cc_final: 0.8758 (t0) REVERT: E 584 ILE cc_start: 0.8930 (pt) cc_final: 0.8695 (mp) REVERT: E 587 ARG cc_start: 0.8948 (mtp-110) cc_final: 0.8689 (mtp-110) REVERT: E 591 ASP cc_start: 0.8870 (m-30) cc_final: 0.8486 (m-30) REVERT: E 618 ASN cc_start: 0.6595 (p0) cc_final: 0.5651 (t0) REVERT: K 87 TYR cc_start: 0.8474 (m-80) cc_final: 0.8157 (m-10) REVERT: I 67 PHE cc_start: 0.8814 (m-80) cc_final: 0.8460 (m-10) REVERT: I 80 LEU cc_start: 0.9785 (tp) cc_final: 0.9316 (tp) REVERT: C 33 ILE cc_start: 0.8939 (mt) cc_final: 0.8534 (mt) REVERT: C 49 ASP cc_start: 0.9013 (p0) cc_final: 0.8534 (p0) REVERT: C 163 ASP cc_start: 0.8737 (t0) cc_final: 0.8435 (t0) REVERT: F 584 ILE cc_start: 0.9170 (pt) cc_final: 0.8964 (mp) REVERT: F 587 ARG cc_start: 0.9050 (mtp-110) cc_final: 0.8724 (mtp-110) REVERT: F 591 ASP cc_start: 0.9011 (m-30) cc_final: 0.8581 (m-30) REVERT: L 33 TRP cc_start: 0.7240 (m-10) cc_final: 0.6860 (m-10) REVERT: L 87 TYR cc_start: 0.8311 (m-10) cc_final: 0.7667 (m-10) REVERT: J 67 PHE cc_start: 0.8638 (m-80) cc_final: 0.8412 (m-80) REVERT: J 79 TYR cc_start: 0.8569 (m-80) cc_final: 0.8352 (m-80) outliers start: 4 outliers final: 0 residues processed: 244 average time/residue: 0.3002 time to fit residues: 100.9838 Evaluate side-chains 144 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 560 GLN D 602 HIS ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN E 560 GLN E 602 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13914 Z= 0.335 Angle : 0.779 10.513 18930 Z= 0.388 Chirality : 0.048 0.348 2166 Planarity : 0.006 0.052 2382 Dihedral : 10.963 78.449 2376 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.14 % Allowed : 2.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.20), residues: 1653 helix: -0.44 (0.34), residues: 213 sheet: -2.79 (0.19), residues: 480 loop : -2.15 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 103 HIS 0.010 0.002 HIS D 602 PHE 0.015 0.002 PHE G 100E TYR 0.021 0.002 TYR K 88 ARG 0.011 0.001 ARG F 596 *********************** 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 198 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.447 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: A 33 ILE cc_start: 0.8986 (mt) cc_final: 0.8775 (mm) REVERT: D 551 GLN cc_start: 0.8629 (tp40) cc_final: 0.8262 (tp-100) REVERT: D 591 ASP cc_start: 0.8958 (m-30) cc_final: 0.8569 (m-30) REVERT: H 46 LYS cc_start: 0.9253 (ptmt) cc_final: 0.8978 (ptmm) REVERT: G 32 TYR cc_start: 0.8782 (m-80) cc_final: 0.8049 (m-80) REVERT: G 45 LEU cc_start: 0.8998 (mm) cc_final: 0.8697 (mm) REVERT: G 67 PHE cc_start: 0.8652 (m-10) cc_final: 0.8433 (m-80) REVERT: B 49 ASP cc_start: 0.8557 (p0) cc_final: 0.8288 (p0) REVERT: B 86 TRP cc_start: 0.9057 (m-10) cc_final: 0.8249 (m-90) REVERT: B 163 ASP cc_start: 0.9186 (t0) cc_final: 0.8855 (t0) REVERT: E 584 ILE cc_start: 0.9205 (pt) cc_final: 0.8988 (mp) REVERT: E 587 ARG cc_start: 0.9027 (mtp-110) cc_final: 0.8402 (ttp80) REVERT: E 591 ASP cc_start: 0.9158 (m-30) cc_final: 0.7998 (m-30) REVERT: E 602 HIS cc_start: 0.8925 (t-90) cc_final: 0.8307 (t70) REVERT: C 33 ILE cc_start: 0.8953 (mt) cc_final: 0.8320 (mm) REVERT: C 53 CYS cc_start: 0.9427 (m) cc_final: 0.8677 (m) REVERT: C 86 TRP cc_start: 0.8926 (m-90) cc_final: 0.8004 (m-90) REVERT: C 163 ASP cc_start: 0.8918 (t0) cc_final: 0.8631 (t0) REVERT: F 588 LYS cc_start: 0.9377 (tppt) cc_final: 0.9152 (tttt) REVERT: F 591 ASP cc_start: 0.9153 (m-30) cc_final: 0.8748 (m-30) REVERT: L 33 TRP cc_start: 0.7879 (m-10) cc_final: 0.7112 (m-10) REVERT: J 32 TYR cc_start: 0.9059 (m-80) cc_final: 0.8831 (m-80) REVERT: J 34 MET cc_start: 0.8379 (mmt) cc_final: 0.8177 (mmt) REVERT: J 45 LEU cc_start: 0.8866 (mm) cc_final: 0.8560 (mm) REVERT: J 79 TYR cc_start: 0.8575 (m-80) cc_final: 0.8174 (m-80) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.3150 time to fit residues: 85.4415 Evaluate side-chains 125 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** A 224 ASN D 521 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13914 Z= 0.372 Angle : 0.776 8.976 18930 Z= 0.390 Chirality : 0.049 0.257 2166 Planarity : 0.005 0.053 2382 Dihedral : 9.904 78.844 2376 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.20), residues: 1653 helix: -0.24 (0.33), residues: 213 sheet: -2.42 (0.20), residues: 471 loop : -2.07 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 275 HIS 0.006 0.001 HIS B 238 PHE 0.015 0.002 PHE K 72 TYR 0.023 0.002 TYR K 87 ARG 0.014 0.001 ARG L 19 *********************** 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 173 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.636 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: D 587 ARG cc_start: 0.9158 (mtp-110) cc_final: 0.8384 (ttp80) REVERT: D 591 ASP cc_start: 0.9124 (m-30) cc_final: 0.8331 (m-30) REVERT: H 46 LYS cc_start: 0.9332 (ptmt) cc_final: 0.9018 (ptmm) REVERT: B 55 ASP cc_start: 0.9498 (m-30) cc_final: 0.9275 (m-30) REVERT: E 591 ASP cc_start: 0.9417 (m-30) cc_final: 0.8916 (m-30) REVERT: K 46 LYS cc_start: 0.9346 (pttt) cc_final: 0.9105 (ptmm) REVERT: C 49 ASP cc_start: 0.8326 (p0) cc_final: 0.8080 (p0) REVERT: C 99 TYR cc_start: 0.8962 (p90) cc_final: 0.8606 (p90) REVERT: F 591 ASP cc_start: 0.9055 (m-30) cc_final: 0.8692 (m-30) REVERT: J 45 LEU cc_start: 0.9055 (mm) cc_final: 0.8718 (mm) REVERT: J 79 TYR cc_start: 0.8587 (m-80) cc_final: 0.8328 (m-80) outliers start: 2 outliers final: 0 residues processed: 173 average time/residue: 0.3101 time to fit residues: 74.8384 Evaluate side-chains 107 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.4980 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 HIS ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13914 Z= 0.402 Angle : 0.794 9.026 18930 Z= 0.398 Chirality : 0.049 0.236 2166 Planarity : 0.005 0.056 2382 Dihedral : 9.450 77.987 2376 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 0.21 % Allowed : 3.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1653 helix: -0.12 (0.33), residues: 213 sheet: -2.13 (0.22), residues: 477 loop : -1.94 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 275 HIS 0.007 0.001 HIS B 238 PHE 0.027 0.002 PHE J 67 TYR 0.026 0.002 TYR H 88 ARG 0.007 0.001 ARG F 587 *********************** 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 167 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9387 (m-30) cc_final: 0.9117 (m-30) REVERT: A 253 LEU cc_start: 0.9548 (mt) cc_final: 0.9200 (tt) REVERT: D 587 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8434 (ttp80) REVERT: D 591 ASP cc_start: 0.9289 (m-30) cc_final: 0.8542 (m-30) REVERT: G 67 PHE cc_start: 0.8364 (m-80) cc_final: 0.7279 (m-80) REVERT: G 82 MET cc_start: 0.8891 (mmp) cc_final: 0.8441 (mmp) REVERT: B 55 ASP cc_start: 0.9479 (m-30) cc_final: 0.9202 (m-30) REVERT: B 163 ASP cc_start: 0.9296 (t70) cc_final: 0.8915 (p0) REVERT: B 253 LEU cc_start: 0.9464 (mt) cc_final: 0.9139 (tt) REVERT: E 591 ASP cc_start: 0.9406 (m-30) cc_final: 0.8997 (m-30) REVERT: K 46 LYS cc_start: 0.9405 (ptmm) cc_final: 0.9151 (ptmm) REVERT: C 55 ASP cc_start: 0.9365 (m-30) cc_final: 0.9156 (m-30) REVERT: C 99 TYR cc_start: 0.9024 (p90) cc_final: 0.8453 (p90) REVERT: C 163 ASP cc_start: 0.9051 (t70) cc_final: 0.8836 (t0) REVERT: C 253 LEU cc_start: 0.9420 (mt) cc_final: 0.9101 (tt) REVERT: F 564 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8166 (mp0) REVERT: F 587 ARG cc_start: 0.9077 (mtp-110) cc_final: 0.8501 (ttp80) REVERT: F 591 ASP cc_start: 0.9304 (m-30) cc_final: 0.8526 (m-30) REVERT: L 46 LYS cc_start: 0.9413 (ptmm) cc_final: 0.9209 (ptmm) REVERT: J 45 LEU cc_start: 0.8962 (mm) cc_final: 0.8527 (mm) REVERT: J 79 TYR cc_start: 0.8587 (m-80) cc_final: 0.8122 (m-80) outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.3088 time to fit residues: 71.2686 Evaluate side-chains 115 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 GLN H 38 GLN B 39 HIS E 521 GLN C 40 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13914 Z= 0.221 Angle : 0.685 9.193 18930 Z= 0.342 Chirality : 0.047 0.231 2166 Planarity : 0.005 0.053 2382 Dihedral : 9.103 80.464 2376 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.07 % Allowed : 1.61 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.21), residues: 1653 helix: 0.04 (0.34), residues: 213 sheet: -1.82 (0.24), residues: 441 loop : -1.89 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 615 HIS 0.004 0.001 HIS D 602 PHE 0.020 0.002 PHE J 67 TYR 0.024 0.002 TYR L 88 ARG 0.005 0.001 ARG E 587 *********************** 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 177 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9386 (m-30) cc_final: 0.9117 (m-30) REVERT: A 99 TYR cc_start: 0.8613 (p90) cc_final: 0.8389 (p90) REVERT: A 253 LEU cc_start: 0.9525 (mt) cc_final: 0.9181 (tt) REVERT: D 521 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8570 (tm-30) REVERT: H 46 LYS cc_start: 0.9337 (ptmt) cc_final: 0.9079 (ptmm) REVERT: B 55 ASP cc_start: 0.9486 (m-30) cc_final: 0.9219 (m-30) REVERT: B 163 ASP cc_start: 0.9249 (t70) cc_final: 0.8886 (p0) REVERT: B 253 LEU cc_start: 0.9409 (mt) cc_final: 0.9109 (tt) REVERT: E 591 ASP cc_start: 0.9405 (m-30) cc_final: 0.8988 (m-30) REVERT: C 55 ASP cc_start: 0.9364 (m-30) cc_final: 0.9161 (m-30) REVERT: C 99 TYR cc_start: 0.8834 (p90) cc_final: 0.8342 (p90) REVERT: C 130 ARG cc_start: 0.8913 (mpp80) cc_final: 0.8587 (mpp80) REVERT: C 163 ASP cc_start: 0.8997 (t70) cc_final: 0.8577 (t0) REVERT: C 253 LEU cc_start: 0.9357 (mt) cc_final: 0.9031 (tt) REVERT: F 587 ARG cc_start: 0.9120 (mtp-110) cc_final: 0.8627 (ttp80) REVERT: F 591 ASP cc_start: 0.9225 (m-30) cc_final: 0.8535 (m-30) REVERT: L 33 TRP cc_start: 0.8366 (m-10) cc_final: 0.7868 (m-10) REVERT: J 45 LEU cc_start: 0.8900 (mm) cc_final: 0.8419 (mm) REVERT: J 79 TYR cc_start: 0.8415 (m-80) cc_final: 0.8170 (m-80) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.3129 time to fit residues: 75.7690 Evaluate side-chains 122 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN D 595 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13914 Z= 0.182 Angle : 0.646 9.347 18930 Z= 0.320 Chirality : 0.045 0.213 2166 Planarity : 0.004 0.049 2382 Dihedral : 8.504 82.727 2376 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.21), residues: 1653 helix: 0.31 (0.35), residues: 213 sheet: -1.68 (0.24), residues: 453 loop : -1.72 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 615 HIS 0.008 0.001 HIS B 39 PHE 0.015 0.001 PHE J 67 TYR 0.025 0.001 TYR H 88 ARG 0.007 0.001 ARG D 587 *********************** 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 178 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.625 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: A 55 ASP cc_start: 0.9394 (m-30) cc_final: 0.9108 (m-30) REVERT: A 99 TYR cc_start: 0.8529 (p90) cc_final: 0.8271 (p90) REVERT: A 253 LEU cc_start: 0.9481 (mt) cc_final: 0.9152 (tt) REVERT: D 521 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 607 ASP cc_start: 0.8979 (m-30) cc_final: 0.8646 (p0) REVERT: G 45 LEU cc_start: 0.9009 (mm) cc_final: 0.8804 (mm) REVERT: B 55 ASP cc_start: 0.9493 (m-30) cc_final: 0.9216 (m-30) REVERT: B 163 ASP cc_start: 0.9178 (t70) cc_final: 0.8898 (p0) REVERT: B 253 LEU cc_start: 0.9402 (mt) cc_final: 0.9110 (tt) REVERT: E 548 MET cc_start: 0.8988 (mpp) cc_final: 0.8712 (mpp) REVERT: K 46 LYS cc_start: 0.9344 (ptmm) cc_final: 0.9139 (ptmm) REVERT: C 55 ASP cc_start: 0.9372 (m-30) cc_final: 0.9167 (m-30) REVERT: C 99 TYR cc_start: 0.8798 (p90) cc_final: 0.8297 (p90) REVERT: C 130 ARG cc_start: 0.8918 (mpp80) cc_final: 0.8587 (mpp80) REVERT: C 163 ASP cc_start: 0.8943 (t70) cc_final: 0.8512 (t0) REVERT: C 253 LEU cc_start: 0.9343 (mt) cc_final: 0.9027 (tt) REVERT: F 561 LEU cc_start: 0.9389 (tt) cc_final: 0.8925 (tt) REVERT: F 587 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8666 (ttp80) REVERT: F 591 ASP cc_start: 0.9198 (m-30) cc_final: 0.8534 (m-30) REVERT: L 33 TRP cc_start: 0.8313 (m-10) cc_final: 0.7835 (m-10) REVERT: J 45 LEU cc_start: 0.8821 (mm) cc_final: 0.8249 (mm) REVERT: J 79 TYR cc_start: 0.8519 (m-80) cc_final: 0.8295 (m-80) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.3019 time to fit residues: 74.4643 Evaluate side-chains 133 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN D 595 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 13914 Z= 0.184 Angle : 0.658 9.364 18930 Z= 0.326 Chirality : 0.045 0.212 2166 Planarity : 0.005 0.048 2382 Dihedral : 8.142 82.777 2376 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.21), residues: 1653 helix: 0.45 (0.35), residues: 213 sheet: -1.51 (0.24), residues: 453 loop : -1.66 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 615 HIS 0.010 0.001 HIS F 602 PHE 0.023 0.001 PHE J 100E TYR 0.022 0.001 TYR L 88 ARG 0.011 0.001 ARG G 97 *********************** 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 178 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 177 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9384 (m-30) cc_final: 0.9105 (m-30) REVERT: A 99 TYR cc_start: 0.8629 (p90) cc_final: 0.8341 (p90) REVERT: A 253 LEU cc_start: 0.9453 (mt) cc_final: 0.9124 (tt) REVERT: D 521 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 607 ASP cc_start: 0.8943 (m-30) cc_final: 0.8622 (p0) REVERT: B 55 ASP cc_start: 0.9515 (m-30) cc_final: 0.9230 (m-30) REVERT: B 163 ASP cc_start: 0.9161 (t70) cc_final: 0.8938 (p0) REVERT: B 253 LEU cc_start: 0.9406 (mt) cc_final: 0.9164 (tt) REVERT: E 587 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8620 (ttp80) REVERT: K 46 LYS cc_start: 0.9322 (ptmm) cc_final: 0.8521 (pptt) REVERT: K 47 LEU cc_start: 0.8906 (tt) cc_final: 0.8705 (tt) REVERT: I 32 TYR cc_start: 0.8613 (m-80) cc_final: 0.8325 (m-80) REVERT: I 103 TRP cc_start: 0.8496 (m100) cc_final: 0.8041 (m100) REVERT: C 99 TYR cc_start: 0.8767 (p90) cc_final: 0.8278 (p90) REVERT: C 130 ARG cc_start: 0.8935 (mpp80) cc_final: 0.8600 (mpp80) REVERT: C 163 ASP cc_start: 0.8898 (t70) cc_final: 0.8481 (t0) REVERT: C 253 LEU cc_start: 0.9315 (mt) cc_final: 0.8930 (tt) REVERT: F 561 LEU cc_start: 0.9370 (tt) cc_final: 0.9150 (tt) REVERT: L 33 TRP cc_start: 0.8345 (m-10) cc_final: 0.7874 (m-10) REVERT: L 46 LYS cc_start: 0.9264 (ptmm) cc_final: 0.8708 (pptt) REVERT: J 45 LEU cc_start: 0.8684 (mm) cc_final: 0.8166 (mm) REVERT: J 79 TYR cc_start: 0.8548 (m-80) cc_final: 0.8315 (m-80) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.3037 time to fit residues: 75.7699 Evaluate side-chains 134 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 116 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 97 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 GLN ** E 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13914 Z= 0.173 Angle : 0.662 9.390 18930 Z= 0.332 Chirality : 0.045 0.231 2166 Planarity : 0.005 0.059 2382 Dihedral : 7.822 83.149 2376 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1653 helix: 0.12 (0.35), residues: 213 sheet: -1.40 (0.24), residues: 459 loop : -1.56 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP G 103 HIS 0.003 0.001 HIS D 516 PHE 0.030 0.001 PHE J 100E TYR 0.023 0.001 TYR K 88 ARG 0.010 0.001 ARG G 97 *********************** 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 185 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.547 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: symmetry clash REVERT: A 55 ASP cc_start: 0.9382 (m-30) cc_final: 0.9097 (m-30) REVERT: A 130 ARG cc_start: 0.9124 (mpp80) cc_final: 0.8575 (mpp80) REVERT: D 521 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8585 (tm-30) REVERT: D 561 LEU cc_start: 0.9188 (tt) cc_final: 0.8974 (tt) REVERT: B 55 ASP cc_start: 0.9510 (m-30) cc_final: 0.9213 (m-30) REVERT: E 548 MET cc_start: 0.8968 (mpp) cc_final: 0.8622 (mpp) REVERT: K 46 LYS cc_start: 0.9332 (ptmm) cc_final: 0.8698 (pptt) REVERT: C 99 TYR cc_start: 0.8719 (p90) cc_final: 0.8227 (p90) REVERT: C 130 ARG cc_start: 0.8936 (mpp80) cc_final: 0.8654 (mpp80) REVERT: C 253 LEU cc_start: 0.9322 (mt) cc_final: 0.8906 (tt) REVERT: F 521 GLN cc_start: 0.9091 (tm-30) cc_final: 0.8674 (tm-30) REVERT: F 587 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8123 (ttp80) REVERT: L 33 TRP cc_start: 0.8314 (m-10) cc_final: 0.7873 (m-10) REVERT: L 46 LYS cc_start: 0.9262 (ptmm) cc_final: 0.8790 (pptt) REVERT: J 79 TYR cc_start: 0.8580 (m-80) cc_final: 0.8350 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2991 time to fit residues: 77.5181 Evaluate side-chains 135 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 595 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 521 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13914 Z= 0.191 Angle : 0.667 9.426 18930 Z= 0.334 Chirality : 0.045 0.223 2166 Planarity : 0.005 0.058 2382 Dihedral : 7.582 82.437 2376 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1653 helix: 0.02 (0.35), residues: 213 sheet: -1.31 (0.24), residues: 459 loop : -1.52 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP G 103 HIS 0.004 0.001 HIS D 613 PHE 0.031 0.002 PHE J 100E TYR 0.023 0.001 TYR K 88 ARG 0.009 0.001 ARG G 97 ********************** 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 169 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9388 (m-30) cc_final: 0.9099 (m-30) REVERT: A 99 TYR cc_start: 0.8585 (p90) cc_final: 0.8328 (p90) REVERT: D 521 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8600 (tm-30) REVERT: H 46 LYS cc_start: 0.9285 (ptmt) cc_final: 0.9073 (ptmm) REVERT: G 32 TYR cc_start: 0.9004 (m-80) cc_final: 0.8719 (m-80) REVERT: B 55 ASP cc_start: 0.9509 (m-30) cc_final: 0.9195 (m-30) REVERT: E 548 MET cc_start: 0.9032 (mpp) cc_final: 0.8577 (mpp) REVERT: E 587 ARG cc_start: 0.8967 (ttp80) cc_final: 0.8207 (ttp80) REVERT: K 46 LYS cc_start: 0.9341 (ptmm) cc_final: 0.8692 (pptt) REVERT: I 103 TRP cc_start: 0.8575 (m100) cc_final: 0.7985 (m100) REVERT: C 99 TYR cc_start: 0.8758 (p90) cc_final: 0.8237 (p90) REVERT: C 130 ARG cc_start: 0.9010 (mpp80) cc_final: 0.8675 (mpp80) REVERT: C 253 LEU cc_start: 0.9334 (mt) cc_final: 0.9071 (tt) REVERT: L 46 LYS cc_start: 0.9276 (ptmm) cc_final: 0.8803 (pptt) REVERT: J 32 TYR cc_start: 0.8908 (m-80) cc_final: 0.8591 (m-80) REVERT: J 79 TYR cc_start: 0.8630 (m-80) cc_final: 0.8394 (m-80) REVERT: J 102 TYR cc_start: 0.8054 (m-80) cc_final: 0.7738 (m-10) outliers start: 1 outliers final: 0 residues processed: 169 average time/residue: 0.2974 time to fit residues: 70.4715 Evaluate side-chains 129 residues out of total 1428 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.041011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.033193 restraints weight = 111609.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.034144 restraints weight = 70101.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.034764 restraints weight = 50565.372| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13914 Z= 0.257 Angle : 0.683 9.326 18930 Z= 0.345 Chirality : 0.045 0.228 2166 Planarity : 0.005 0.060 2382 Dihedral : 7.408 79.617 2376 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.21), residues: 1653 helix: 0.12 (0.36), residues: 210 sheet: -1.14 (0.24), residues: 453 loop : -1.51 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 103 HIS 0.004 0.001 HIS B 238 PHE 0.031 0.002 PHE J 100E TYR 0.024 0.002 TYR K 88 ARG 0.010 0.001 ARG G 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.97 seconds wall clock time: 50 minutes 10.60 seconds (3010.60 seconds total)