Starting phenix.real_space_refine on Thu Jul 31 20:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzm_8936/07_2025/6dzm_8936.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzm_8936/07_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_8936/07_2025/6dzm_8936.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzm_8936/07_2025/6dzm_8936.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzm_8936/07_2025/6dzm_8936.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzm_8936/07_2025/6dzm_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.81, per 1000 atoms: 0.50 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=6, 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 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 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: 1.56 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: 3.55 Time building geometry restraints manager: 4.02 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: 8195 23.20 - 46.39: 166 46.39 - 69.59: 45 69.59 - 92.79: 24 92.79 - 115.98: 12 Dihedral angle restraints: 8442 sinusoidal: 3597 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 8439 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: 240 2.59 - 3.16: 12302 3.16 - 3.74: 21055 3.74 - 4.32: 29663 4.32 - 4.90: 47127 Nonbonded interactions: 110387 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 110382 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } 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' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } 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: 2.570 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.480 Find NCS groups from input model: 0.240 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- 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 13947 Z= 0.350 Angle : 0.996 13.676 19023 Z= 0.502 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02158 ( 12) link_NAG-ASN : angle 4.35536 ( 36) 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_ALPHA1-3 : bond 0.00466 ( 3) link_ALPHA1-3 : angle 1.86241 ( 9) hydrogen bonds : bond 0.23347 ( 387) hydrogen bonds : angle 10.40260 ( 999) SS BOND : bond 0.00616 ( 6) SS BOND : angle 1.07642 ( 12) covalent geometry : bond 0.00782 (13914) covalent geometry : angle 0.95646 (18930) *********************** 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 : 1.452 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: 0.4077 time to fit residues: 169.3330 Evaluate side-chains 144 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.8982 ------------------------------------------------------------------------------- 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 ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.047866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.039894 restraints weight = 110913.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040914 restraints weight = 72675.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.041662 restraints weight = 53161.013| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13947 Z= 0.173 Angle : 0.833 13.382 19023 Z= 0.407 Chirality : 0.050 0.249 2166 Planarity : 0.007 0.060 2382 Dihedral : 12.312 80.833 2376 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % 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: -1.05 (0.33), residues: 213 sheet: -3.19 (0.18), residues: 477 loop : -2.39 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 103 HIS 0.005 0.001 HIS J 100D PHE 0.019 0.002 PHE J 67 TYR 0.020 0.002 TYR H 88 ARG 0.007 0.001 ARG J 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00914 ( 12) link_NAG-ASN : angle 3.56287 ( 36) link_ALPHA1-6 : bond 0.00783 ( 3) link_ALPHA1-6 : angle 1.32729 ( 9) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 3.57298 ( 27) link_ALPHA1-3 : bond 0.01626 ( 3) link_ALPHA1-3 : angle 1.29231 ( 9) hydrogen bonds : bond 0.04993 ( 387) hydrogen bonds : angle 7.03419 ( 999) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.31089 ( 12) covalent geometry : bond 0.00365 (13914) covalent geometry : angle 0.80817 (18930) *********************** 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 246 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 242 time to evaluate : 1.506 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: A 33 ILE cc_start: 0.9001 (mt) cc_final: 0.8694 (mm) REVERT: A 49 ASP cc_start: 0.8837 (p0) cc_final: 0.8437 (p0) REVERT: A 163 ASP cc_start: 0.8869 (t0) cc_final: 0.8571 (t0) REVERT: D 567 GLN cc_start: 0.9475 (tt0) cc_final: 0.9075 (tm-30) REVERT: D 571 LEU cc_start: 0.9280 (mt) cc_final: 0.8852 (mt) REVERT: D 591 ASP cc_start: 0.8935 (m-30) cc_final: 0.8596 (m-30) REVERT: D 602 HIS cc_start: 0.9115 (m-70) cc_final: 0.8867 (t70) REVERT: H 87 TYR cc_start: 0.8375 (m-10) cc_final: 0.8025 (m-80) REVERT: G 32 TYR cc_start: 0.8865 (m-80) cc_final: 0.8168 (m-80) REVERT: B 33 ILE cc_start: 0.8981 (mt) cc_final: 0.8673 (mm) REVERT: B 49 ASP cc_start: 0.8753 (p0) cc_final: 0.8337 (p0) REVERT: B 163 ASP cc_start: 0.8878 (t0) cc_final: 0.8415 (t0) REVERT: E 584 ILE cc_start: 0.8910 (pt) cc_final: 0.8640 (mp) REVERT: E 587 ARG cc_start: 0.8941 (mtp-110) cc_final: 0.8711 (mtp-110) REVERT: E 591 ASP cc_start: 0.8877 (m-30) cc_final: 0.8544 (m-30) REVERT: E 618 ASN cc_start: 0.7091 (p0) cc_final: 0.6104 (t0) REVERT: K 87 TYR cc_start: 0.8570 (m-80) cc_final: 0.8205 (m-10) REVERT: I 67 PHE cc_start: 0.8812 (m-80) cc_final: 0.8475 (m-10) REVERT: I 80 LEU cc_start: 0.9777 (tp) cc_final: 0.9283 (tp) REVERT: C 33 ILE cc_start: 0.8983 (mt) cc_final: 0.8617 (mt) REVERT: C 49 ASP cc_start: 0.9034 (p0) cc_final: 0.8558 (p0) REVERT: C 163 ASP cc_start: 0.8424 (t0) cc_final: 0.8195 (t0) REVERT: F 584 ILE cc_start: 0.9168 (pt) cc_final: 0.8951 (mp) REVERT: F 587 ARG cc_start: 0.9009 (mtp-110) cc_final: 0.8727 (mtp-110) REVERT: F 591 ASP cc_start: 0.9028 (m-30) cc_final: 0.8641 (m-30) REVERT: L 33 TRP cc_start: 0.7310 (m-10) cc_final: 0.6926 (m-10) REVERT: L 87 TYR cc_start: 0.8371 (m-10) cc_final: 0.7712 (m-10) REVERT: J 45 LEU cc_start: 0.8958 (mm) cc_final: 0.8697 (mm) outliers start: 4 outliers final: 0 residues processed: 245 average time/residue: 0.3024 time to fit residues: 102.0992 Evaluate side-chains 141 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN D 560 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN 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 F 602 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.045011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.037097 restraints weight = 112322.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038125 restraints weight = 72388.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.038871 restraints weight = 52362.829| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13947 Z= 0.187 Angle : 0.767 10.552 19023 Z= 0.375 Chirality : 0.047 0.311 2166 Planarity : 0.006 0.051 2382 Dihedral : 10.565 79.740 2376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.14 % Allowed : 2.80 % Favored : 97.06 % 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: -3.15 (0.20), residues: 1653 helix: -0.35 (0.34), residues: 213 sheet: -2.79 (0.19), residues: 477 loop : -2.14 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 103 HIS 0.007 0.001 HIS E 602 PHE 0.014 0.002 PHE G 29 TYR 0.017 0.002 TYR K 88 ARG 0.012 0.001 ARG F 596 Details of bonding type rmsd link_NAG-ASN : bond 0.01036 ( 12) link_NAG-ASN : angle 2.98574 ( 36) link_ALPHA1-6 : bond 0.00727 ( 3) link_ALPHA1-6 : angle 2.26680 ( 9) link_BETA1-4 : bond 0.00522 ( 9) link_BETA1-4 : angle 3.45380 ( 27) link_ALPHA1-3 : bond 0.00722 ( 3) link_ALPHA1-3 : angle 1.70506 ( 9) hydrogen bonds : bond 0.04212 ( 387) hydrogen bonds : angle 6.42151 ( 999) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.32784 ( 12) covalent geometry : bond 0.00406 (13914) covalent geometry : angle 0.74379 (18930) *********************** 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 203 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.9392 (m-30) cc_final: 0.9169 (p0) REVERT: D 587 ARG cc_start: 0.9095 (mtp-110) cc_final: 0.8409 (ttp80) REVERT: D 591 ASP cc_start: 0.9000 (m-30) cc_final: 0.8250 (m-30) REVERT: H 46 LYS cc_start: 0.9244 (ptmt) cc_final: 0.9001 (ptmm) REVERT: H 87 TYR cc_start: 0.8656 (m-10) cc_final: 0.8423 (m-10) REVERT: G 32 TYR cc_start: 0.8752 (m-80) cc_final: 0.7768 (m-80) REVERT: G 45 LEU cc_start: 0.8986 (mm) cc_final: 0.8611 (mm) REVERT: G 82 MET cc_start: 0.8678 (mmp) cc_final: 0.8447 (mmp) REVERT: B 33 ILE cc_start: 0.8906 (mt) cc_final: 0.8456 (mm) REVERT: B 86 TRP cc_start: 0.8871 (m-10) cc_final: 0.8082 (m-90) REVERT: B 163 ASP cc_start: 0.8920 (t0) cc_final: 0.8560 (t0) REVERT: E 584 ILE cc_start: 0.9181 (pt) cc_final: 0.8908 (mp) REVERT: E 587 ARG cc_start: 0.8962 (mtp-110) cc_final: 0.8333 (ttp80) REVERT: E 591 ASP cc_start: 0.9099 (m-30) cc_final: 0.8259 (m-30) REVERT: E 602 HIS cc_start: 0.8986 (t-90) cc_final: 0.8321 (t70) REVERT: K 87 TYR cc_start: 0.8829 (m-80) cc_final: 0.8437 (m-10) REVERT: C 33 ILE cc_start: 0.8937 (mt) cc_final: 0.8713 (mm) REVERT: C 49 ASP cc_start: 0.8614 (p0) cc_final: 0.8330 (p0) REVERT: C 53 CYS cc_start: 0.9391 (m) cc_final: 0.9016 (m) REVERT: F 548 MET cc_start: 0.8750 (mtp) cc_final: 0.8249 (tpp) REVERT: F 587 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8859 (mtp-110) REVERT: F 591 ASP cc_start: 0.9142 (m-30) cc_final: 0.8750 (m-30) REVERT: L 33 TRP cc_start: 0.7869 (m-10) cc_final: 0.7178 (m-10) REVERT: L 87 TYR cc_start: 0.8590 (m-10) cc_final: 0.7903 (m-10) REVERT: J 45 LEU cc_start: 0.8825 (mm) cc_final: 0.8493 (mm) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.3257 time to fit residues: 90.5143 Evaluate side-chains 125 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 44 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 = 0.3175 r_free = 0.3175 target = 0.044225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.036143 restraints weight = 113268.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.037185 restraints weight = 71690.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.037934 restraints weight = 51312.331| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13947 Z= 0.174 Angle : 0.717 9.195 19023 Z= 0.350 Chirality : 0.046 0.241 2166 Planarity : 0.005 0.051 2382 Dihedral : 9.436 80.824 2376 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.14 % Allowed : 1.96 % 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 (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: -2.71 (0.20), residues: 1653 helix: 0.03 (0.35), residues: 213 sheet: -2.31 (0.20), residues: 501 loop : -1.94 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 86 HIS 0.004 0.001 HIS E 516 PHE 0.016 0.002 PHE G 67 TYR 0.020 0.002 TYR L 88 ARG 0.013 0.001 ARG K 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00888 ( 12) link_NAG-ASN : angle 2.83286 ( 36) link_ALPHA1-6 : bond 0.00844 ( 3) link_ALPHA1-6 : angle 1.94796 ( 9) link_BETA1-4 : bond 0.00554 ( 9) link_BETA1-4 : angle 3.18690 ( 27) link_ALPHA1-3 : bond 0.01139 ( 3) link_ALPHA1-3 : angle 1.36252 ( 9) hydrogen bonds : bond 0.03815 ( 387) hydrogen bonds : angle 6.19119 ( 999) SS BOND : bond 0.00297 ( 6) SS BOND : angle 0.40694 ( 12) covalent geometry : bond 0.00374 (13914) covalent geometry : angle 0.69526 (18930) *********************** 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 188 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 587 ARG cc_start: 0.9017 (mtp-110) cc_final: 0.8452 (ttp80) REVERT: D 591 ASP cc_start: 0.9091 (m-30) cc_final: 0.8499 (m-30) REVERT: H 46 LYS cc_start: 0.9318 (ptmt) cc_final: 0.9053 (ptmm) REVERT: G 32 TYR cc_start: 0.8826 (m-80) cc_final: 0.8139 (m-80) REVERT: B 86 TRP cc_start: 0.8994 (m-10) cc_final: 0.8258 (m-90) REVERT: E 584 ILE cc_start: 0.9214 (pt) cc_final: 0.8923 (mp) REVERT: E 587 ARG cc_start: 0.8970 (mtp-110) cc_final: 0.8502 (ttp80) REVERT: E 591 ASP cc_start: 0.9161 (m-30) cc_final: 0.8366 (m-30) REVERT: E 602 HIS cc_start: 0.9040 (t-90) cc_final: 0.8376 (t70) REVERT: K 46 LYS cc_start: 0.9361 (pttt) cc_final: 0.9097 (ptmm) REVERT: I 82 MET cc_start: 0.8792 (mmp) cc_final: 0.8453 (mmp) REVERT: C 33 ILE cc_start: 0.8987 (mt) cc_final: 0.8666 (mm) REVERT: F 588 LYS cc_start: 0.9328 (tppt) cc_final: 0.9042 (tttm) REVERT: F 591 ASP cc_start: 0.9060 (m-30) cc_final: 0.8709 (m-30) REVERT: L 33 TRP cc_start: 0.8089 (m-10) cc_final: 0.7575 (m-10) REVERT: L 46 LYS cc_start: 0.9278 (ptmt) cc_final: 0.9076 (ptmm) REVERT: J 45 LEU cc_start: 0.9009 (mm) cc_final: 0.8611 (mm) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.3044 time to fit residues: 79.7156 Evaluate side-chains 120 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 38 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN ** 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 = 0.3154 r_free = 0.3154 target = 0.043590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.035543 restraints weight = 112559.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.036584 restraints weight = 70468.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037333 restraints weight = 50552.709| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13947 Z= 0.160 Angle : 0.687 9.282 19023 Z= 0.337 Chirality : 0.046 0.233 2166 Planarity : 0.005 0.051 2382 Dihedral : 8.625 81.604 2376 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.21 % Allowed : 2.31 % Favored : 97.48 % 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: -2.50 (0.20), residues: 1653 helix: 0.21 (0.35), residues: 213 sheet: -2.13 (0.20), residues: 513 loop : -1.81 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 86 HIS 0.004 0.001 HIS E 516 PHE 0.014 0.002 PHE I 67 TYR 0.037 0.002 TYR B 162 ARG 0.007 0.001 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 12) link_NAG-ASN : angle 2.62410 ( 36) link_ALPHA1-6 : bond 0.00768 ( 3) link_ALPHA1-6 : angle 1.69735 ( 9) link_BETA1-4 : bond 0.00525 ( 9) link_BETA1-4 : angle 3.10387 ( 27) link_ALPHA1-3 : bond 0.01122 ( 3) link_ALPHA1-3 : angle 1.26189 ( 9) hydrogen bonds : bond 0.03559 ( 387) hydrogen bonds : angle 6.07192 ( 999) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.48007 ( 12) covalent geometry : bond 0.00347 (13914) covalent geometry : angle 0.66741 (18930) *********************** 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 188 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 1.537 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: 0.9584 (mt) cc_final: 0.9300 (tt) REVERT: D 587 ARG cc_start: 0.9041 (mtp-110) cc_final: 0.8372 (ttp80) REVERT: D 591 ASP cc_start: 0.9096 (m-30) cc_final: 0.8274 (m-30) REVERT: G 28 THR cc_start: 0.8892 (p) cc_final: 0.8522 (p) REVERT: G 32 TYR cc_start: 0.9072 (m-80) cc_final: 0.8447 (m-80) REVERT: B 86 TRP cc_start: 0.9083 (m-10) cc_final: 0.8442 (m-90) REVERT: B 163 ASP cc_start: 0.9103 (t70) cc_final: 0.8853 (t0) REVERT: B 253 LEU cc_start: 0.9530 (mt) cc_final: 0.9233 (tt) REVERT: B 255 GLN cc_start: 0.9470 (mt0) cc_final: 0.9265 (mt0) REVERT: E 584 ILE cc_start: 0.9281 (pt) cc_final: 0.9029 (mp) REVERT: E 618 ASN cc_start: 0.7495 (p0) cc_final: 0.7282 (p0) REVERT: I 32 TYR cc_start: 0.9083 (m-10) cc_final: 0.8829 (m-10) REVERT: I 79 TYR cc_start: 0.8763 (m-80) cc_final: 0.8536 (m-10) REVERT: C 253 LEU cc_start: 0.9428 (mt) cc_final: 0.9165 (tt) REVERT: F 587 ARG cc_start: 0.9062 (mtp-110) cc_final: 0.8442 (ttp80) REVERT: F 591 ASP cc_start: 0.9139 (m-30) cc_final: 0.8521 (m-30) REVERT: L 33 TRP cc_start: 0.8271 (m-10) cc_final: 0.7730 (m-10) REVERT: J 82 MET cc_start: 0.9169 (mmp) cc_final: 0.8849 (mmp) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.3032 time to fit residues: 78.3003 Evaluate side-chains 120 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 154 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 128 optimal weight: 0.1980 chunk 106 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 586 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.042991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.034897 restraints weight = 114171.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.035930 restraints weight = 71088.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036666 restraints weight = 50947.864| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13947 Z= 0.178 Angle : 0.688 9.179 19023 Z= 0.339 Chirality : 0.045 0.241 2166 Planarity : 0.005 0.052 2382 Dihedral : 8.323 80.952 2376 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % 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 (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: -2.33 (0.21), residues: 1653 helix: 0.19 (0.35), residues: 213 sheet: -1.91 (0.21), residues: 513 loop : -1.74 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 615 HIS 0.004 0.001 HIS I 100D PHE 0.027 0.002 PHE I 67 TYR 0.021 0.002 TYR H 88 ARG 0.008 0.001 ARG A 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00817 ( 12) link_NAG-ASN : angle 2.49239 ( 36) link_ALPHA1-6 : bond 0.00860 ( 3) link_ALPHA1-6 : angle 1.62075 ( 9) link_BETA1-4 : bond 0.00491 ( 9) link_BETA1-4 : angle 3.07307 ( 27) link_ALPHA1-3 : bond 0.01092 ( 3) link_ALPHA1-3 : angle 1.15139 ( 9) hydrogen bonds : bond 0.03610 ( 387) hydrogen bonds : angle 5.98088 ( 999) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.52163 ( 12) covalent geometry : bond 0.00385 (13914) covalent geometry : angle 0.66989 (18930) *********************** 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 180 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.401 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: A 99 TYR cc_start: 0.8771 (p90) cc_final: 0.8567 (p90) REVERT: A 253 LEU cc_start: 0.9585 (mt) cc_final: 0.9282 (tt) REVERT: D 561 LEU cc_start: 0.9363 (tt) cc_final: 0.8963 (tt) REVERT: G 28 THR cc_start: 0.8867 (p) cc_final: 0.8489 (p) REVERT: G 32 TYR cc_start: 0.9026 (m-80) cc_final: 0.8377 (m-80) REVERT: B 49 ASP cc_start: 0.8816 (p0) cc_final: 0.8588 (p0) REVERT: B 130 ARG cc_start: 0.8846 (mpp80) cc_final: 0.8645 (mpp80) REVERT: B 163 ASP cc_start: 0.9053 (t70) cc_final: 0.8721 (t0) REVERT: B 253 LEU cc_start: 0.9539 (mt) cc_final: 0.9286 (tt) REVERT: E 607 ASP cc_start: 0.9007 (m-30) cc_final: 0.8651 (p0) REVERT: E 618 ASN cc_start: 0.7334 (p0) cc_final: 0.7066 (p0) REVERT: K 46 LYS cc_start: 0.9341 (ptmm) cc_final: 0.9107 (ptmm) REVERT: I 79 TYR cc_start: 0.8693 (m-80) cc_final: 0.8480 (m-10) REVERT: I 80 LEU cc_start: 0.9776 (tp) cc_final: 0.9256 (tt) REVERT: C 49 ASP cc_start: 0.8553 (p0) cc_final: 0.8332 (p0) REVERT: C 253 LEU cc_start: 0.9500 (mt) cc_final: 0.9187 (tt) REVERT: F 587 ARG cc_start: 0.9006 (mtp-110) cc_final: 0.8518 (ttp80) REVERT: F 591 ASP cc_start: 0.9041 (m-30) cc_final: 0.8406 (m-30) REVERT: L 46 LYS cc_start: 0.9316 (ptmm) cc_final: 0.8836 (pptt) REVERT: J 45 LEU cc_start: 0.8948 (mm) cc_final: 0.8529 (mm) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3000 time to fit residues: 75.2782 Evaluate side-chains 120 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 48 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 0.0770 chunk 116 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN D 521 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** J 100DHIS ** 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 = 0.3143 r_free = 0.3143 target = 0.043069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.034845 restraints weight = 110730.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035890 restraints weight = 69400.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.036628 restraints weight = 49776.421| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13947 Z= 0.112 Angle : 0.660 9.418 19023 Z= 0.320 Chirality : 0.045 0.211 2166 Planarity : 0.005 0.049 2382 Dihedral : 7.920 83.416 2376 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 0.77 % Favored : 99.16 % 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: -2.17 (0.21), residues: 1653 helix: 0.34 (0.35), residues: 213 sheet: -1.61 (0.22), residues: 498 loop : -1.78 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 33 HIS 0.003 0.001 HIS I 100D PHE 0.014 0.001 PHE J 67 TYR 0.021 0.001 TYR L 88 ARG 0.007 0.001 ARG D 587 Details of bonding type rmsd link_NAG-ASN : bond 0.00890 ( 12) link_NAG-ASN : angle 2.20584 ( 36) link_ALPHA1-6 : bond 0.00890 ( 3) link_ALPHA1-6 : angle 1.69453 ( 9) link_BETA1-4 : bond 0.00597 ( 9) link_BETA1-4 : angle 2.82591 ( 27) link_ALPHA1-3 : bond 0.01134 ( 3) link_ALPHA1-3 : angle 1.03029 ( 9) hydrogen bonds : bond 0.03466 ( 387) hydrogen bonds : angle 5.79711 ( 999) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.42546 ( 12) covalent geometry : bond 0.00241 (13914) covalent geometry : angle 0.64383 (18930) *********************** 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 202 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 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: A 99 TYR cc_start: 0.8537 (p90) cc_final: 0.8315 (p90) REVERT: A 253 LEU cc_start: 0.9561 (mt) cc_final: 0.9263 (tt) REVERT: D 521 GLN cc_start: 0.9157 (tm130) cc_final: 0.8767 (tm-30) REVERT: G 28 THR cc_start: 0.8983 (p) cc_final: 0.8606 (p) REVERT: G 32 TYR cc_start: 0.9052 (m-80) cc_final: 0.8366 (m-80) REVERT: G 45 LEU cc_start: 0.9061 (mm) cc_final: 0.8742 (mm) REVERT: G 67 PHE cc_start: 0.7991 (m-80) cc_final: 0.7744 (m-80) REVERT: G 82 MET cc_start: 0.9128 (mmp) cc_final: 0.8601 (mmp) REVERT: B 86 TRP cc_start: 0.9155 (m-10) cc_final: 0.8461 (m-90) REVERT: B 99 TYR cc_start: 0.8411 (p90) cc_final: 0.7959 (p90) REVERT: B 130 ARG cc_start: 0.8902 (mpp80) cc_final: 0.8673 (mpp80) REVERT: B 163 ASP cc_start: 0.9081 (t70) cc_final: 0.8763 (t0) REVERT: B 253 LEU cc_start: 0.9551 (mt) cc_final: 0.9313 (tt) REVERT: E 607 ASP cc_start: 0.9028 (m-30) cc_final: 0.8668 (p0) REVERT: E 618 ASN cc_start: 0.7695 (p0) cc_final: 0.7331 (p0) REVERT: K 46 LYS cc_start: 0.9478 (ptmm) cc_final: 0.8927 (pptt) REVERT: K 47 LEU cc_start: 0.8691 (pp) cc_final: 0.8204 (pp) REVERT: I 34 MET cc_start: 0.8755 (mpp) cc_final: 0.8487 (mpp) REVERT: I 79 TYR cc_start: 0.8647 (m-80) cc_final: 0.8425 (m-10) REVERT: I 103 TRP cc_start: 0.8697 (m100) cc_final: 0.8223 (m100) REVERT: C 130 ARG cc_start: 0.8719 (mpp80) cc_final: 0.8487 (mpp80) REVERT: C 163 ASP cc_start: 0.8809 (t70) cc_final: 0.8484 (t0) REVERT: C 253 LEU cc_start: 0.9451 (mt) cc_final: 0.9121 (tt) REVERT: F 561 LEU cc_start: 0.9311 (tt) cc_final: 0.8966 (tt) REVERT: F 587 ARG cc_start: 0.9001 (mtp-110) cc_final: 0.8621 (ttp80) REVERT: F 591 ASP cc_start: 0.8995 (m-30) cc_final: 0.8403 (m-30) REVERT: L 33 TRP cc_start: 0.8397 (m-10) cc_final: 0.7916 (m-10) REVERT: J 32 TYR cc_start: 0.9060 (m-80) cc_final: 0.8838 (m-80) REVERT: J 45 LEU cc_start: 0.9007 (mm) cc_final: 0.8635 (mm) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.3023 time to fit residues: 84.3961 Evaluate side-chains 140 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 87 optimal weight: 4.9990 chunk 153 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 chunk 159 optimal weight: 0.0870 chunk 144 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.8168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN ** J 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.042923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.034639 restraints weight = 113332.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.035648 restraints weight = 71769.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.036379 restraints weight = 52014.998| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13947 Z= 0.124 Angle : 0.659 9.377 19023 Z= 0.322 Chirality : 0.044 0.211 2166 Planarity : 0.005 0.048 2382 Dihedral : 7.732 82.998 2376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.06 (0.21), residues: 1653 helix: 0.46 (0.36), residues: 210 sheet: -1.50 (0.23), residues: 474 loop : -1.75 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP G 103 HIS 0.006 0.001 HIS C 39 PHE 0.017 0.001 PHE J 67 TYR 0.024 0.001 TYR L 88 ARG 0.011 0.001 ARG I 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 12) link_NAG-ASN : angle 2.24410 ( 36) link_ALPHA1-6 : bond 0.00888 ( 3) link_ALPHA1-6 : angle 1.58113 ( 9) link_BETA1-4 : bond 0.00522 ( 9) link_BETA1-4 : angle 2.87559 ( 27) link_ALPHA1-3 : bond 0.01017 ( 3) link_ALPHA1-3 : angle 1.16929 ( 9) hydrogen bonds : bond 0.03235 ( 387) hydrogen bonds : angle 5.73256 ( 999) SS BOND : bond 0.00217 ( 6) SS BOND : angle 0.53202 ( 12) covalent geometry : bond 0.00274 (13914) covalent geometry : angle 0.64310 (18930) *********************** 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 182 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.571 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 253 LEU cc_start: 0.9543 (mt) cc_final: 0.9226 (tt) REVERT: D 521 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8694 (tm-30) REVERT: D 561 LEU cc_start: 0.9361 (tt) cc_final: 0.9020 (tt) REVERT: G 28 THR cc_start: 0.9149 (p) cc_final: 0.8793 (p) REVERT: G 32 TYR cc_start: 0.9074 (m-80) cc_final: 0.8397 (m-80) REVERT: G 79 TYR cc_start: 0.9023 (m-10) cc_final: 0.8701 (m-10) REVERT: B 55 ASP cc_start: 0.9561 (m-30) cc_final: 0.9355 (m-30) REVERT: B 163 ASP cc_start: 0.9041 (t70) cc_final: 0.8762 (t0) REVERT: B 253 LEU cc_start: 0.9527 (mt) cc_final: 0.9303 (tt) REVERT: E 607 ASP cc_start: 0.9109 (m-30) cc_final: 0.8689 (p0) REVERT: E 618 ASN cc_start: 0.7738 (p0) cc_final: 0.7351 (p0) REVERT: K 46 LYS cc_start: 0.9463 (ptmm) cc_final: 0.8863 (pptt) REVERT: K 47 LEU cc_start: 0.8723 (pp) cc_final: 0.8225 (pp) REVERT: I 34 MET cc_start: 0.8717 (mpp) cc_final: 0.8447 (mpp) REVERT: I 79 TYR cc_start: 0.8716 (m-80) cc_final: 0.8491 (m-10) REVERT: I 103 TRP cc_start: 0.8709 (m100) cc_final: 0.8188 (m100) REVERT: C 163 ASP cc_start: 0.8754 (t70) cc_final: 0.8488 (t0) REVERT: C 253 LEU cc_start: 0.9435 (mt) cc_final: 0.9094 (tt) REVERT: F 561 LEU cc_start: 0.9359 (tt) cc_final: 0.9007 (tt) REVERT: F 587 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8544 (ttp80) REVERT: F 591 ASP cc_start: 0.8998 (m-30) cc_final: 0.8432 (m-30) REVERT: L 33 TRP cc_start: 0.8414 (m-10) cc_final: 0.7922 (m-10) REVERT: J 45 LEU cc_start: 0.8976 (mm) cc_final: 0.8582 (mm) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2887 time to fit residues: 74.3702 Evaluate side-chains 131 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 0.0770 chunk 124 optimal weight: 6.9990 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 521 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.041668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.033618 restraints weight = 113157.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.034603 restraints weight = 71111.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.035328 restraints weight = 51317.214| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13947 Z= 0.174 Angle : 0.679 9.239 19023 Z= 0.334 Chirality : 0.045 0.216 2166 Planarity : 0.005 0.052 2382 Dihedral : 7.689 80.051 2376 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % 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: -1.95 (0.21), residues: 1653 helix: 0.42 (0.35), residues: 213 sheet: -1.48 (0.24), residues: 459 loop : -1.62 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 103 HIS 0.004 0.001 HIS F 516 PHE 0.023 0.002 PHE J 67 TYR 0.022 0.002 TYR K 88 ARG 0.011 0.001 ARG G 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 12) link_NAG-ASN : angle 2.23015 ( 36) link_ALPHA1-6 : bond 0.00894 ( 3) link_ALPHA1-6 : angle 1.54793 ( 9) link_BETA1-4 : bond 0.00446 ( 9) link_BETA1-4 : angle 2.99226 ( 27) link_ALPHA1-3 : bond 0.00767 ( 3) link_ALPHA1-3 : angle 1.35677 ( 9) hydrogen bonds : bond 0.03427 ( 387) hydrogen bonds : angle 5.73515 ( 999) SS BOND : bond 0.00278 ( 6) SS BOND : angle 0.65896 ( 12) covalent geometry : bond 0.00379 (13914) covalent geometry : angle 0.66244 (18930) *********************** 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 170 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.397 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 253 LEU cc_start: 0.9546 (mt) cc_final: 0.9227 (tt) REVERT: D 521 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8502 (tm-30) REVERT: H 46 LYS cc_start: 0.9236 (pptt) cc_final: 0.9022 (pptt) REVERT: G 28 THR cc_start: 0.9179 (p) cc_final: 0.8828 (p) REVERT: G 32 TYR cc_start: 0.9096 (m-80) cc_final: 0.8423 (m-80) REVERT: B 55 ASP cc_start: 0.9541 (m-30) cc_final: 0.9325 (m-30) REVERT: B 253 LEU cc_start: 0.9516 (mt) cc_final: 0.9286 (tt) REVERT: E 587 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8532 (ttp80) REVERT: E 607 ASP cc_start: 0.9176 (m-30) cc_final: 0.8759 (p0) REVERT: K 46 LYS cc_start: 0.9460 (ptmm) cc_final: 0.8903 (pptt) REVERT: K 47 LEU cc_start: 0.8716 (pp) cc_final: 0.8259 (pp) REVERT: I 79 TYR cc_start: 0.8694 (m-80) cc_final: 0.8444 (m-10) REVERT: I 82 MET cc_start: 0.8975 (mmp) cc_final: 0.8643 (mmp) REVERT: C 253 LEU cc_start: 0.9445 (mt) cc_final: 0.9095 (tt) REVERT: F 561 LEU cc_start: 0.9449 (tt) cc_final: 0.9065 (tt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2810 time to fit residues: 67.9512 Evaluate side-chains 121 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 109 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 42 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 521 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** J 100DHIS ** 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 = 0.3121 r_free = 0.3121 target = 0.042944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.034762 restraints weight = 108867.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.035802 restraints weight = 68072.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.036548 restraints weight = 48844.005| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 13947 Z= 0.120 Angle : 0.666 9.420 19023 Z= 0.327 Chirality : 0.045 0.216 2166 Planarity : 0.005 0.059 2382 Dihedral : 7.547 81.268 2376 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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: -1.90 (0.21), residues: 1653 helix: 0.38 (0.35), residues: 213 sheet: -1.41 (0.24), residues: 459 loop : -1.57 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 103 HIS 0.008 0.001 HIS F 602 PHE 0.013 0.001 PHE J 100E TYR 0.024 0.001 TYR K 88 ARG 0.009 0.001 ARG G 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 12) link_NAG-ASN : angle 2.30082 ( 36) link_ALPHA1-6 : bond 0.00927 ( 3) link_ALPHA1-6 : angle 1.55675 ( 9) link_BETA1-4 : bond 0.00509 ( 9) link_BETA1-4 : angle 2.81637 ( 27) link_ALPHA1-3 : bond 0.01001 ( 3) link_ALPHA1-3 : angle 1.26269 ( 9) hydrogen bonds : bond 0.03420 ( 387) hydrogen bonds : angle 5.71489 ( 999) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.53028 ( 12) covalent geometry : bond 0.00272 (13914) covalent geometry : angle 0.64938 (18930) ********************** 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 174 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.511 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 253 LEU cc_start: 0.9514 (mt) cc_final: 0.9278 (tt) REVERT: D 521 GLN cc_start: 0.9158 (tm130) cc_final: 0.8782 (tm-30) REVERT: H 46 LYS cc_start: 0.9208 (pptt) cc_final: 0.9001 (pptt) REVERT: G 28 THR cc_start: 0.9139 (p) cc_final: 0.8778 (p) REVERT: G 32 TYR cc_start: 0.9101 (m-80) cc_final: 0.8447 (m-80) REVERT: B 55 ASP cc_start: 0.9538 (m-30) cc_final: 0.9316 (m-30) REVERT: B 253 LEU cc_start: 0.9502 (mt) cc_final: 0.9294 (tt) REVERT: E 607 ASP cc_start: 0.9195 (m-30) cc_final: 0.8787 (p0) REVERT: I 32 TYR cc_start: 0.8508 (m-80) cc_final: 0.8149 (m-80) REVERT: I 79 TYR cc_start: 0.8669 (m-80) cc_final: 0.8428 (m-10) REVERT: I 103 TRP cc_start: 0.8563 (m100) cc_final: 0.7719 (m100) REVERT: C 253 LEU cc_start: 0.9416 (mt) cc_final: 0.8980 (tt) REVERT: F 561 LEU cc_start: 0.9410 (tt) cc_final: 0.9031 (tt) REVERT: F 587 ARG cc_start: 0.8660 (ttp80) cc_final: 0.7969 (ttp80) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.2737 time to fit residues: 68.2504 Evaluate side-chains 126 residues out of total 1428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100DHIS ** 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 = 0.3129 r_free = 0.3129 target = 0.043351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.035257 restraints weight = 113721.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.036304 restraints weight = 70913.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037049 restraints weight = 50996.442| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13947 Z= 0.116 Angle : 0.675 9.497 19023 Z= 0.330 Chirality : 0.045 0.213 2166 Planarity : 0.005 0.057 2382 Dihedral : 7.457 81.802 2376 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % 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: -1.81 (0.21), residues: 1653 helix: 0.45 (0.35), residues: 213 sheet: -1.28 (0.24), residues: 459 loop : -1.56 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 103 HIS 0.003 0.001 HIS F 516 PHE 0.031 0.001 PHE J 67 TYR 0.024 0.001 TYR K 88 ARG 0.014 0.001 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00822 ( 12) link_NAG-ASN : angle 2.25734 ( 36) link_ALPHA1-6 : bond 0.00809 ( 3) link_ALPHA1-6 : angle 1.51363 ( 9) link_BETA1-4 : bond 0.00526 ( 9) link_BETA1-4 : angle 2.73253 ( 27) link_ALPHA1-3 : bond 0.00944 ( 3) link_ALPHA1-3 : angle 1.27403 ( 9) hydrogen bonds : bond 0.03673 ( 387) hydrogen bonds : angle 5.68409 ( 999) SS BOND : bond 0.00179 ( 6) SS BOND : angle 0.50750 ( 12) covalent geometry : bond 0.00258 (13914) covalent geometry : angle 0.65943 (18930) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.71 seconds wall clock time: 70 minutes 57.15 seconds (4257.15 seconds total)