Starting phenix.real_space_refine on Tue Nov 18 09:14:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzl_8935/11_2025/6dzl_8935.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 8040 2.51 5 N 2100 2.21 5 O 2511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12693 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1664 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 712 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "J" 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: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" 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 Restraints were copied for chains: B, C, E, F, K, L, H, I, O, Q, P, R Time building chain proxies: 2.72, per 1000 atoms: 0.21 Number of scatterers: 12693 At special positions: 0 Unit cell: (136.85, 139.15, 85.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 2511 8.00 N 2100 7.00 C 8040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.04 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN P 4 " - " MAN P 5 " " MAN R 4 " - " MAN R 5 " 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 6 " " BMA P 3 " - " MAN P 6 " " BMA R 3 " - " MAN R 6 " 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 40 " " NAG A 404 " - " ASN A 238 " " NAG B 403 " - " ASN B 40 " " NAG B 404 " - " ASN B 238 " " NAG C 403 " - " ASN C 40 " " NAG C 404 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 637.6 milliseconds 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2886 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 36 sheets defined 15.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.726A pdb=" N THR A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE D 555 " --> pdb=" O GLN D 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS D 556 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 Processing helix chain 'J' and resid 80 through 84 removed outlier: 3.765A pdb=" N ALA J 84 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 79 through 85 removed outlier: 3.725A pdb=" N THR B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR B 261 " --> pdb=" O ASN B 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE E 555 " --> pdb=" O GLN E 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS E 556 " --> pdb=" O ASP E 552 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.764A pdb=" N ALA K 84 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 79 through 85 removed outlier: 3.727A pdb=" N THR C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 264 removed outlier: 4.125A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR C 261 " --> pdb=" O ASN C 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 575 removed outlier: 4.030A pdb=" N ILE F 555 " --> pdb=" O GLN F 551 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS F 556 " --> pdb=" O ASP F 552 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.765A pdb=" N ALA L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.936A pdb=" N VAL A 37 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 44 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.506A pdb=" N VAL A 97 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 114 removed outlier: 7.047A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.532A pdb=" N THR A 223 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 515 through 516 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.489A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU J 33 " --> pdb=" O SER J 49 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 17 through 20 removed outlier: 3.567A pdb=" N SER G 70 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.671A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA G 93 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 39 removed outlier: 3.937A pdb=" N VAL B 37 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN B 44 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 64 through 69 Processing sheet with id=AB6, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.506A pdb=" N VAL B 97 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 108 through 114 removed outlier: 7.046A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.531A pdb=" N THR B 223 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 515 through 516 Processing sheet with id=AC1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.311A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.490A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU K 33 " --> pdb=" O SER K 49 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 17 through 20 removed outlier: 3.568A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.671A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.936A pdb=" N VAL C 37 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN C 44 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 64 through 69 Processing sheet with id=AC9, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.505A pdb=" N VAL C 97 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 108 through 114 removed outlier: 7.046A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 220 through 223 removed outlier: 3.532A pdb=" N THR C 223 " --> pdb=" O GLU C 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 515 through 516 Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.310A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.488A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 17 through 20 removed outlier: 3.568A pdb=" N SER I 70 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.670A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA I 93 " --> pdb=" O SER I 35 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.62 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: 4020 1.34 - 1.46: 3431 1.46 - 1.58: 5485 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 12987 Sorted by residual: bond pdb=" C PHE A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.336 1.309 0.026 1.23e-02 6.61e+03 4.64e+00 bond pdb=" C PHE C 132 " pdb=" N PRO C 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.12e+00 bond pdb=" C PHE B 132 " pdb=" N PRO B 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.08e+00 bond pdb=" CA ARG C 134 " pdb=" CB ARG C 134 " ideal model delta sigma weight residual 1.527 1.480 0.047 2.48e-02 1.63e+03 3.61e+00 bond pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta sigma weight residual 1.533 1.490 0.043 2.29e-02 1.91e+03 3.49e+00 ... (remaining 12982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16447 1.73 - 3.45: 1013 3.45 - 5.18: 159 5.18 - 6.90: 21 6.90 - 8.63: 9 Bond angle restraints: 17649 Sorted by residual: angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.10 109.66 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.10 109.73 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N ALA J 51 " pdb=" CA ALA J 51 " pdb=" CB ALA J 51 " ideal model delta sigma weight residual 114.10 109.75 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N GLY D 524 " pdb=" CA GLY D 524 " pdb=" C GLY D 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 angle pdb=" N GLY F 524 " pdb=" CA GLY F 524 " pdb=" C GLY F 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 ... (remaining 17644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 7770 22.65 - 45.29: 192 45.29 - 67.94: 6 67.94 - 90.58: 18 90.58 - 113.23: 12 Dihedral angle restraints: 7998 sinusoidal: 3462 harmonic: 4536 Sorted by residual: dihedral pdb=" CA LEU A 51 " pdb=" C LEU A 51 " pdb=" N VAL A 52 " pdb=" CA VAL A 52 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 51 " pdb=" C LEU C 51 " pdb=" N VAL C 52 " pdb=" CA VAL C 52 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU B 51 " pdb=" C LEU B 51 " pdb=" N VAL B 52 " pdb=" CA VAL B 52 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 7995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 2028 0.317 - 0.634: 3 0.634 - 0.951: 0 0.951 - 1.268: 0 1.268 - 1.585: 3 Chirality restraints: 2034 Sorted by residual: chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 238 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.81 -1.59 2.00e-01 2.50e+01 6.28e+01 chirality pdb=" C1 NAG A 404 " pdb=" ND2 ASN A 238 " pdb=" C2 NAG A 404 " pdb=" O5 NAG A 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.26e+01 chirality pdb=" C1 NAG B 404 " pdb=" ND2 ASN B 238 " pdb=" C2 NAG B 404 " pdb=" O5 NAG B 404 " both_signs ideal model delta sigma weight residual False -2.40 -0.83 -1.57 2.00e-01 2.50e+01 6.19e+01 ... (remaining 2031 not shown) Planarity restraints: 2232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.065 2.00e-02 2.50e+03 7.76e-02 7.53e+01 pdb=" CG ASN C 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.129 2.00e-02 2.50e+03 pdb=" C1 NAG C 404 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 238 " -0.064 2.00e-02 2.50e+03 7.74e-02 7.49e+01 pdb=" CG ASN A 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 238 " 0.129 2.00e-02 2.50e+03 pdb=" C1 NAG A 404 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 238 " -0.064 2.00e-02 2.50e+03 7.70e-02 7.41e+01 pdb=" CG ASN B 238 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 238 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN B 238 " 0.128 2.00e-02 2.50e+03 pdb=" C1 NAG B 404 " -0.093 2.00e-02 2.50e+03 ... (remaining 2229 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 280 2.63 - 3.20: 12522 3.20 - 3.77: 19679 3.77 - 4.33: 26990 4.33 - 4.90: 43975 Nonbonded interactions: 103446 Sorted by model distance: nonbonded pdb=" O SER K 49 " pdb=" OD2 ASP K 50 " model vdw 2.069 3.040 nonbonded pdb=" O SER J 49 " pdb=" OD2 ASP J 50 " model vdw 2.069 3.040 nonbonded pdb=" O SER L 49 " pdb=" OD2 ASP L 50 " model vdw 2.070 3.040 nonbonded pdb=" OG SER K 52 " pdb=" O6 MAN P 5 " model vdw 2.246 3.040 nonbonded pdb=" OG SER J 52 " pdb=" O6 MAN N 5 " model vdw 2.246 3.040 ... (remaining 103441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.020 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.012 0.073 13032 Z= 0.533 Angle : 1.008 12.220 17769 Z= 0.512 Chirality : 0.080 1.585 2034 Planarity : 0.006 0.050 2220 Dihedral : 11.385 113.229 5067 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.18), residues: 1557 helix: -1.99 (0.33), residues: 177 sheet: -3.80 (0.16), residues: 468 loop : -2.87 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 559 TYR 0.017 0.003 TYR A 109 PHE 0.017 0.003 PHE K 71 TRP 0.019 0.003 TRP G 47 HIS 0.004 0.001 HIS I 100D Details of bonding type rmsd covalent geometry : bond 0.01161 (12987) covalent geometry : angle 0.95357 (17649) SS BOND : bond 0.00487 ( 15) SS BOND : angle 1.14991 ( 30) hydrogen bonds : bond 0.23990 ( 324) hydrogen bonds : angle 11.24842 ( 891) link_ALPHA1-2 : bond 0.00393 ( 3) link_ALPHA1-2 : angle 2.56540 ( 9) link_ALPHA1-3 : bond 0.00271 ( 3) link_ALPHA1-3 : angle 3.03537 ( 9) link_ALPHA1-6 : bond 0.00349 ( 3) link_ALPHA1-6 : angle 1.79626 ( 9) link_BETA1-4 : bond 0.01202 ( 9) link_BETA1-4 : angle 2.35592 ( 27) link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 6.76171 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LYS cc_start: 0.9802 (mttt) cc_final: 0.9585 (mttp) REVERT: D 591 ASP cc_start: 0.8916 (m-30) cc_final: 0.8649 (m-30) REVERT: G 39 GLN cc_start: 0.9536 (tt0) cc_final: 0.9238 (tt0) REVERT: H 39 GLN cc_start: 0.9558 (tt0) cc_final: 0.9250 (tt0) REVERT: C 84 LYS cc_start: 0.9776 (mttt) cc_final: 0.9552 (mttp) REVERT: I 39 GLN cc_start: 0.9471 (tt0) cc_final: 0.9140 (tt0) outliers start: 3 outliers final: 0 residues processed: 242 average time/residue: 0.1616 time to fit residues: 51.6909 Evaluate side-chains 96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.037174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.030253 restraints weight = 94945.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.031395 restraints weight = 50314.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.032172 restraints weight = 32726.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032756 restraints weight = 24329.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033201 restraints weight = 19434.892| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13032 Z= 0.161 Angle : 0.699 8.644 17769 Z= 0.345 Chirality : 0.046 0.319 2034 Planarity : 0.005 0.042 2220 Dihedral : 9.752 73.994 2337 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.20), residues: 1557 helix: -0.67 (0.40), residues: 177 sheet: -2.82 (0.20), residues: 450 loop : -2.25 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.015 0.002 TYR J 91 PHE 0.017 0.001 PHE D 572 TRP 0.008 0.001 TRP E 518 HIS 0.006 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00347 (12987) covalent geometry : angle 0.66336 (17649) SS BOND : bond 0.00520 ( 15) SS BOND : angle 1.95879 ( 30) hydrogen bonds : bond 0.03827 ( 324) hydrogen bonds : angle 7.11538 ( 891) link_ALPHA1-2 : bond 0.00357 ( 3) link_ALPHA1-2 : angle 1.68008 ( 9) link_ALPHA1-3 : bond 0.01403 ( 3) link_ALPHA1-3 : angle 2.00142 ( 9) link_ALPHA1-6 : bond 0.00179 ( 3) link_ALPHA1-6 : angle 2.06410 ( 9) link_BETA1-4 : bond 0.00531 ( 9) link_BETA1-4 : angle 1.91219 ( 27) link_NAG-ASN : bond 0.00672 ( 12) link_NAG-ASN : angle 4.09204 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 ASP cc_start: 0.8269 (m-30) cc_final: 0.7924 (m-30) REVERT: G 39 GLN cc_start: 0.9603 (tt0) cc_final: 0.9079 (tm-30) REVERT: G 51 ILE cc_start: 0.9582 (tt) cc_final: 0.9336 (tp) REVERT: B 69 ASN cc_start: 0.9046 (m-40) cc_final: 0.8807 (m110) REVERT: E 552 ASP cc_start: 0.8509 (m-30) cc_final: 0.8131 (m-30) REVERT: K 27 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8436 (tm-30) REVERT: H 39 GLN cc_start: 0.9626 (tt0) cc_final: 0.9129 (tm-30) REVERT: H 73 ASN cc_start: 0.9256 (p0) cc_final: 0.8830 (m-40) REVERT: H 75 LYS cc_start: 0.9621 (ttmm) cc_final: 0.9363 (ttmm) REVERT: C 69 ASN cc_start: 0.8936 (m-40) cc_final: 0.8629 (m110) REVERT: L 74 THR cc_start: 0.9256 (t) cc_final: 0.8980 (t) REVERT: I 39 GLN cc_start: 0.9553 (tt0) cc_final: 0.9132 (tm-30) REVERT: I 73 ASN cc_start: 0.9110 (p0) cc_final: 0.8810 (m-40) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1307 time to fit residues: 29.0891 Evaluate side-chains 97 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 148 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 0.0030 chunk 131 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 516 HIS E 516 HIS E 551 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.029811 restraints weight = 96417.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.030931 restraints weight = 51768.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.031707 restraints weight = 33969.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.032299 restraints weight = 25310.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.032649 restraints weight = 20175.890| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13032 Z= 0.118 Angle : 0.613 8.004 17769 Z= 0.301 Chirality : 0.044 0.298 2034 Planarity : 0.004 0.058 2220 Dihedral : 8.792 65.874 2337 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.20), residues: 1557 helix: -0.54 (0.39), residues: 177 sheet: -2.19 (0.22), residues: 426 loop : -1.96 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.011 0.001 TYR C 261 PHE 0.009 0.001 PHE D 572 TRP 0.008 0.001 TRP F 518 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00257 (12987) covalent geometry : angle 0.58101 (17649) SS BOND : bond 0.00338 ( 15) SS BOND : angle 1.36655 ( 30) hydrogen bonds : bond 0.03275 ( 324) hydrogen bonds : angle 6.35495 ( 891) link_ALPHA1-2 : bond 0.00347 ( 3) link_ALPHA1-2 : angle 1.57777 ( 9) link_ALPHA1-3 : bond 0.01733 ( 3) link_ALPHA1-3 : angle 1.71164 ( 9) link_ALPHA1-6 : bond 0.00299 ( 3) link_ALPHA1-6 : angle 2.05022 ( 9) link_BETA1-4 : bond 0.00318 ( 9) link_BETA1-4 : angle 1.68278 ( 27) link_NAG-ASN : bond 0.00458 ( 12) link_NAG-ASN : angle 3.75993 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9126 (ptpp) cc_final: 0.8905 (ptpp) REVERT: D 552 ASP cc_start: 0.8229 (m-30) cc_final: 0.7931 (m-30) REVERT: J 83 PHE cc_start: 0.8476 (m-80) cc_final: 0.8220 (m-80) REVERT: G 39 GLN cc_start: 0.9572 (tt0) cc_final: 0.9115 (tt0) REVERT: B 69 ASN cc_start: 0.8983 (m-40) cc_final: 0.8776 (m110) REVERT: E 552 ASP cc_start: 0.8437 (m-30) cc_final: 0.8069 (m-30) REVERT: K 27 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8373 (tm-30) REVERT: H 39 GLN cc_start: 0.9579 (tt0) cc_final: 0.9333 (tt0) REVERT: C 69 ASN cc_start: 0.8885 (m-40) cc_final: 0.8639 (m110) REVERT: F 552 ASP cc_start: 0.7877 (m-30) cc_final: 0.7356 (m-30) REVERT: L 27 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8498 (tm-30) REVERT: L 74 THR cc_start: 0.9219 (t) cc_final: 0.8937 (t) REVERT: L 83 PHE cc_start: 0.8539 (m-80) cc_final: 0.8326 (m-80) REVERT: I 39 GLN cc_start: 0.9518 (tt0) cc_final: 0.9138 (tt0) REVERT: I 83 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8389 (mtm180) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1351 time to fit residues: 24.2257 Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 33 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 GLN G 6 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.028648 restraints weight = 97010.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.029741 restraints weight = 52212.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.030528 restraints weight = 34545.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.031125 restraints weight = 25594.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.031511 restraints weight = 20347.716| |-----------------------------------------------------------------------------| r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13032 Z= 0.127 Angle : 0.590 7.238 17769 Z= 0.288 Chirality : 0.043 0.272 2034 Planarity : 0.004 0.062 2220 Dihedral : 7.917 56.077 2337 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.26 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.21), residues: 1557 helix: -0.08 (0.37), residues: 195 sheet: -2.05 (0.23), residues: 450 loop : -1.75 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 89 TYR 0.012 0.001 TYR A 261 PHE 0.007 0.001 PHE E 582 TRP 0.017 0.001 TRP A 104 HIS 0.004 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00278 (12987) covalent geometry : angle 0.56094 (17649) SS BOND : bond 0.00355 ( 15) SS BOND : angle 1.44199 ( 30) hydrogen bonds : bond 0.03012 ( 324) hydrogen bonds : angle 5.79103 ( 891) link_ALPHA1-2 : bond 0.00314 ( 3) link_ALPHA1-2 : angle 1.65279 ( 9) link_ALPHA1-3 : bond 0.01699 ( 3) link_ALPHA1-3 : angle 1.14284 ( 9) link_ALPHA1-6 : bond 0.00404 ( 3) link_ALPHA1-6 : angle 2.06750 ( 9) link_BETA1-4 : bond 0.00390 ( 9) link_BETA1-4 : angle 1.60583 ( 27) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 3.45607 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8855 (ptpp) REVERT: D 552 ASP cc_start: 0.8246 (m-30) cc_final: 0.7792 (m-30) REVERT: G 39 GLN cc_start: 0.9596 (tt0) cc_final: 0.9088 (tt0) REVERT: G 83 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8374 (mtm180) REVERT: B 69 ASN cc_start: 0.9071 (m-40) cc_final: 0.8769 (m110) REVERT: E 552 ASP cc_start: 0.8500 (m-30) cc_final: 0.7999 (m-30) REVERT: H 39 GLN cc_start: 0.9595 (tt0) cc_final: 0.9182 (tm-30) REVERT: C 69 ASN cc_start: 0.8927 (m-40) cc_final: 0.8610 (m110) REVERT: F 552 ASP cc_start: 0.8158 (m-30) cc_final: 0.7698 (m-30) REVERT: L 83 PHE cc_start: 0.8737 (m-80) cc_final: 0.8333 (m-80) REVERT: I 39 GLN cc_start: 0.9528 (tt0) cc_final: 0.9120 (tm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1373 time to fit residues: 22.4635 Evaluate side-chains 83 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 151 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.032980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.026047 restraints weight = 101450.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.027044 restraints weight = 55875.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.027756 restraints weight = 37463.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.028257 restraints weight = 28279.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.028630 restraints weight = 23063.115| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13032 Z= 0.292 Angle : 0.748 6.768 17769 Z= 0.361 Chirality : 0.046 0.321 2034 Planarity : 0.005 0.059 2220 Dihedral : 8.066 52.893 2337 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1557 helix: -0.01 (0.37), residues: 201 sheet: -2.36 (0.21), residues: 474 loop : -1.50 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.021 0.002 TYR I 90 PHE 0.022 0.002 PHE B 132 TRP 0.015 0.002 TRP H 99 HIS 0.017 0.003 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00623 (12987) covalent geometry : angle 0.72479 (17649) SS BOND : bond 0.00295 ( 15) SS BOND : angle 0.97547 ( 30) hydrogen bonds : bond 0.03696 ( 324) hydrogen bonds : angle 6.00485 ( 891) link_ALPHA1-2 : bond 0.00077 ( 3) link_ALPHA1-2 : angle 2.11737 ( 9) link_ALPHA1-3 : bond 0.01030 ( 3) link_ALPHA1-3 : angle 1.27552 ( 9) link_ALPHA1-6 : bond 0.00078 ( 3) link_ALPHA1-6 : angle 2.11661 ( 9) link_BETA1-4 : bond 0.00804 ( 9) link_BETA1-4 : angle 2.17687 ( 27) link_NAG-ASN : bond 0.00372 ( 12) link_NAG-ASN : angle 3.36041 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.506 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: D 552 ASP cc_start: 0.8471 (m-30) cc_final: 0.8129 (m-30) REVERT: G 39 GLN cc_start: 0.9566 (tt0) cc_final: 0.9139 (tt0) REVERT: B 260 ILE cc_start: 0.8592 (mm) cc_final: 0.8315 (tp) REVERT: E 552 ASP cc_start: 0.8557 (m-30) cc_final: 0.8066 (m-30) REVERT: H 83 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8246 (mtm180) REVERT: F 552 ASP cc_start: 0.8300 (m-30) cc_final: 0.8022 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1385 time to fit residues: 18.2333 Evaluate side-chains 71 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 6 optimal weight: 0.9990 chunk 91 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 150 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 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 = 0.2845 r_free = 0.2845 target = 0.034185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.027109 restraints weight = 96523.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.028166 restraints weight = 52570.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.028914 restraints weight = 35109.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.029463 restraints weight = 26306.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.029849 restraints weight = 21193.564| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13032 Z= 0.114 Angle : 0.597 7.645 17769 Z= 0.292 Chirality : 0.044 0.246 2034 Planarity : 0.004 0.056 2220 Dihedral : 7.418 52.606 2337 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.22), residues: 1557 helix: 0.43 (0.38), residues: 201 sheet: -2.14 (0.21), residues: 552 loop : -1.24 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 18 TYR 0.009 0.001 TYR A 261 PHE 0.012 0.001 PHE C 234 TRP 0.010 0.001 TRP B 104 HIS 0.008 0.002 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00250 (12987) covalent geometry : angle 0.57564 (17649) SS BOND : bond 0.00394 ( 15) SS BOND : angle 1.06761 ( 30) hydrogen bonds : bond 0.02963 ( 324) hydrogen bonds : angle 5.45921 ( 891) link_ALPHA1-2 : bond 0.00090 ( 3) link_ALPHA1-2 : angle 2.31816 ( 9) link_ALPHA1-3 : bond 0.01854 ( 3) link_ALPHA1-3 : angle 0.85699 ( 9) link_ALPHA1-6 : bond 0.00413 ( 3) link_ALPHA1-6 : angle 1.98405 ( 9) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.43554 ( 27) link_NAG-ASN : bond 0.00430 ( 12) link_NAG-ASN : angle 2.86707 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.548 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: D 552 ASP cc_start: 0.8330 (m-30) cc_final: 0.7907 (m-30) REVERT: D 574 ARG cc_start: 0.9417 (ttt180) cc_final: 0.9139 (ttt180) REVERT: J 33 LEU cc_start: 0.8861 (tp) cc_final: 0.8569 (tp) REVERT: G 39 GLN cc_start: 0.9592 (tt0) cc_final: 0.9212 (tm-30) REVERT: G 83 ARG cc_start: 0.8758 (mtm-85) cc_final: 0.8404 (mtm180) REVERT: B 69 ASN cc_start: 0.9030 (m-40) cc_final: 0.8755 (m110) REVERT: B 115 LYS cc_start: 0.9746 (mmtt) cc_final: 0.9501 (tppt) REVERT: B 260 ILE cc_start: 0.8590 (mm) cc_final: 0.8316 (tp) REVERT: E 552 ASP cc_start: 0.8407 (m-30) cc_final: 0.7925 (m-30) REVERT: H 83 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8334 (mtm180) REVERT: C 69 ASN cc_start: 0.9022 (m-40) cc_final: 0.8682 (m110) REVERT: C 260 ILE cc_start: 0.8504 (mm) cc_final: 0.8246 (tp) REVERT: F 552 ASP cc_start: 0.8385 (m-30) cc_final: 0.7793 (m-30) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1655 time to fit residues: 24.1897 Evaluate side-chains 80 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 91 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.033042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.026052 restraints weight = 100171.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.027054 restraints weight = 55441.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.027778 restraints weight = 37276.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.028257 restraints weight = 28223.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.028633 restraints weight = 23118.920| |-----------------------------------------------------------------------------| r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13032 Z= 0.214 Angle : 0.655 6.933 17769 Z= 0.314 Chirality : 0.044 0.276 2034 Planarity : 0.004 0.052 2220 Dihedral : 7.375 55.451 2337 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.22), residues: 1557 helix: 0.57 (0.39), residues: 201 sheet: -2.08 (0.20), residues: 564 loop : -1.26 (0.24), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 574 TYR 0.013 0.001 TYR H 90 PHE 0.013 0.002 PHE K 71 TRP 0.012 0.002 TRP I 99 HIS 0.010 0.002 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00459 (12987) covalent geometry : angle 0.63356 (17649) SS BOND : bond 0.00735 ( 15) SS BOND : angle 1.29768 ( 30) hydrogen bonds : bond 0.03160 ( 324) hydrogen bonds : angle 5.48139 ( 891) link_ALPHA1-2 : bond 0.00019 ( 3) link_ALPHA1-2 : angle 2.13502 ( 9) link_ALPHA1-3 : bond 0.01255 ( 3) link_ALPHA1-3 : angle 1.01089 ( 9) link_ALPHA1-6 : bond 0.00264 ( 3) link_ALPHA1-6 : angle 2.12913 ( 9) link_BETA1-4 : bond 0.00596 ( 9) link_BETA1-4 : angle 1.77138 ( 27) link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 2.97283 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.511 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: D 552 ASP cc_start: 0.8363 (m-30) cc_final: 0.7930 (m-30) REVERT: D 555 ILE cc_start: 0.9613 (mp) cc_final: 0.9049 (tt) REVERT: J 33 LEU cc_start: 0.9005 (tp) cc_final: 0.8770 (tp) REVERT: G 83 ARG cc_start: 0.8765 (mtm-85) cc_final: 0.8296 (mtm180) REVERT: B 260 ILE cc_start: 0.8626 (mm) cc_final: 0.8385 (tp) REVERT: E 552 ASP cc_start: 0.8466 (m-30) cc_final: 0.7980 (m-30) REVERT: H 83 ARG cc_start: 0.8810 (mtm-85) cc_final: 0.8331 (mtm180) REVERT: C 69 ASN cc_start: 0.9109 (m-40) cc_final: 0.8622 (m110) REVERT: C 260 ILE cc_start: 0.8502 (mm) cc_final: 0.8269 (tp) REVERT: F 552 ASP cc_start: 0.8521 (m-30) cc_final: 0.7924 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1492 time to fit residues: 19.7975 Evaluate side-chains 71 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 87 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.032733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.025772 restraints weight = 97947.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.026778 restraints weight = 54058.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.027496 restraints weight = 36308.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.027979 restraints weight = 27382.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.028363 restraints weight = 22384.365| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 13032 Z= 0.218 Angle : 0.657 10.542 17769 Z= 0.317 Chirality : 0.044 0.266 2034 Planarity : 0.004 0.052 2220 Dihedral : 7.364 59.054 2337 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.22), residues: 1557 helix: 0.64 (0.39), residues: 201 sheet: -2.04 (0.21), residues: 513 loop : -1.27 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 18 TYR 0.011 0.001 TYR J 91 PHE 0.010 0.002 PHE K 71 TRP 0.013 0.002 TRP H 99 HIS 0.009 0.002 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00467 (12987) covalent geometry : angle 0.63760 (17649) SS BOND : bond 0.00251 ( 15) SS BOND : angle 1.12553 ( 30) hydrogen bonds : bond 0.03206 ( 324) hydrogen bonds : angle 5.43273 ( 891) link_ALPHA1-2 : bond 0.00118 ( 3) link_ALPHA1-2 : angle 2.35299 ( 9) link_ALPHA1-3 : bond 0.01250 ( 3) link_ALPHA1-3 : angle 0.89982 ( 9) link_ALPHA1-6 : bond 0.00271 ( 3) link_ALPHA1-6 : angle 2.12233 ( 9) link_BETA1-4 : bond 0.00569 ( 9) link_BETA1-4 : angle 1.58550 ( 27) link_NAG-ASN : bond 0.00294 ( 12) link_NAG-ASN : angle 2.83392 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.499 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: D 552 ASP cc_start: 0.8508 (m-30) cc_final: 0.8155 (m-30) REVERT: D 555 ILE cc_start: 0.9626 (mp) cc_final: 0.9081 (tt) REVERT: J 33 LEU cc_start: 0.9029 (tp) cc_final: 0.8774 (tp) REVERT: G 83 ARG cc_start: 0.8787 (mtm-85) cc_final: 0.8377 (mtm180) REVERT: B 260 ILE cc_start: 0.8613 (mm) cc_final: 0.8374 (tp) REVERT: E 552 ASP cc_start: 0.8538 (m-30) cc_final: 0.8061 (m-30) REVERT: H 34 MET cc_start: 0.9322 (mmp) cc_final: 0.9011 (mmp) REVERT: H 83 ARG cc_start: 0.8817 (mtm-85) cc_final: 0.8342 (mtm180) REVERT: C 69 ASN cc_start: 0.9108 (m-40) cc_final: 0.8643 (m110) REVERT: C 260 ILE cc_start: 0.8505 (mm) cc_final: 0.8280 (tp) REVERT: F 552 ASP cc_start: 0.8490 (m-30) cc_final: 0.7907 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1414 time to fit residues: 19.0839 Evaluate side-chains 71 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 92 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 0.0000 chunk 3 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.033394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026410 restraints weight = 96318.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.027465 restraints weight = 52205.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.028204 restraints weight = 34633.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.028684 restraints weight = 25881.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.029103 restraints weight = 21086.413| |-----------------------------------------------------------------------------| r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13032 Z= 0.118 Angle : 0.586 8.304 17769 Z= 0.283 Chirality : 0.043 0.228 2034 Planarity : 0.004 0.049 2220 Dihedral : 6.876 59.807 2337 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1557 helix: 0.72 (0.39), residues: 201 sheet: -1.72 (0.22), residues: 483 loop : -1.22 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 18 TYR 0.008 0.001 TYR B 261 PHE 0.008 0.001 PHE B 234 TRP 0.010 0.001 TRP C 104 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00261 (12987) covalent geometry : angle 0.56542 (17649) SS BOND : bond 0.00216 ( 15) SS BOND : angle 1.15578 ( 30) hydrogen bonds : bond 0.02837 ( 324) hydrogen bonds : angle 5.19744 ( 891) link_ALPHA1-2 : bond 0.00041 ( 3) link_ALPHA1-2 : angle 2.58277 ( 9) link_ALPHA1-3 : bond 0.01627 ( 3) link_ALPHA1-3 : angle 0.57354 ( 9) link_ALPHA1-6 : bond 0.00492 ( 3) link_ALPHA1-6 : angle 1.88042 ( 9) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.39750 ( 27) link_NAG-ASN : bond 0.00361 ( 12) link_NAG-ASN : angle 2.69950 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.528 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: D 552 ASP cc_start: 0.8466 (m-30) cc_final: 0.8142 (m-30) REVERT: D 555 ILE cc_start: 0.9601 (mp) cc_final: 0.9005 (tt) REVERT: J 33 LEU cc_start: 0.8982 (tp) cc_final: 0.8689 (tp) REVERT: G 83 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8574 (mtm180) REVERT: B 69 ASN cc_start: 0.9048 (m-40) cc_final: 0.8692 (m110) REVERT: B 260 ILE cc_start: 0.8602 (mm) cc_final: 0.8353 (tp) REVERT: E 552 ASP cc_start: 0.8515 (m-30) cc_final: 0.8032 (m-30) REVERT: E 578 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8006 (pt0) REVERT: H 34 MET cc_start: 0.9340 (mmp) cc_final: 0.9023 (mmp) REVERT: H 95 ASP cc_start: 0.8461 (p0) cc_final: 0.8256 (p0) REVERT: C 69 ASN cc_start: 0.9054 (m-40) cc_final: 0.8603 (m110) REVERT: C 260 ILE cc_start: 0.8616 (mm) cc_final: 0.8399 (tp) REVERT: F 552 ASP cc_start: 0.8432 (m-30) cc_final: 0.7842 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1363 time to fit residues: 18.5373 Evaluate side-chains 71 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.033182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026247 restraints weight = 97884.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.027289 restraints weight = 52849.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.028050 restraints weight = 35000.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028496 restraints weight = 26012.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.028908 restraints weight = 21310.884| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13032 Z= 0.156 Angle : 0.604 8.096 17769 Z= 0.290 Chirality : 0.043 0.231 2034 Planarity : 0.004 0.051 2220 Dihedral : 6.741 59.074 2337 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1557 helix: 0.69 (0.38), residues: 204 sheet: -1.61 (0.22), residues: 483 loop : -1.21 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 83 TYR 0.010 0.001 TYR L 91 PHE 0.009 0.001 PHE B 234 TRP 0.015 0.002 TRP H 99 HIS 0.012 0.002 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00342 (12987) covalent geometry : angle 0.58391 (17649) SS BOND : bond 0.00263 ( 15) SS BOND : angle 1.19050 ( 30) hydrogen bonds : bond 0.02885 ( 324) hydrogen bonds : angle 5.17675 ( 891) link_ALPHA1-2 : bond 0.00069 ( 3) link_ALPHA1-2 : angle 2.47032 ( 9) link_ALPHA1-3 : bond 0.01415 ( 3) link_ALPHA1-3 : angle 0.72366 ( 9) link_ALPHA1-6 : bond 0.00485 ( 3) link_ALPHA1-6 : angle 1.85917 ( 9) link_BETA1-4 : bond 0.00424 ( 9) link_BETA1-4 : angle 1.53957 ( 27) link_NAG-ASN : bond 0.00233 ( 12) link_NAG-ASN : angle 2.72489 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3114 Ramachandran restraints generated. 1557 Oldfield, 0 Emsley, 1557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.519 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: D 552 ASP cc_start: 0.8502 (m-30) cc_final: 0.8283 (m-30) REVERT: D 555 ILE cc_start: 0.9615 (mp) cc_final: 0.9058 (tt) REVERT: J 33 LEU cc_start: 0.8974 (tp) cc_final: 0.8699 (tp) REVERT: G 83 ARG cc_start: 0.8873 (mtm-85) cc_final: 0.8587 (mtm180) REVERT: B 260 ILE cc_start: 0.8638 (mm) cc_final: 0.8401 (tp) REVERT: E 552 ASP cc_start: 0.8567 (m-30) cc_final: 0.8115 (m-30) REVERT: H 34 MET cc_start: 0.9357 (mmp) cc_final: 0.9139 (mmp) REVERT: C 69 ASN cc_start: 0.9006 (m-40) cc_final: 0.8567 (m110) REVERT: C 260 ILE cc_start: 0.8590 (mm) cc_final: 0.8386 (tp) REVERT: F 552 ASP cc_start: 0.8496 (m-30) cc_final: 0.7922 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1376 time to fit residues: 18.1998 Evaluate side-chains 70 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 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 = 0.2826 r_free = 0.2826 target = 0.033714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.026849 restraints weight = 95029.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.027907 restraints weight = 50922.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.028666 restraints weight = 33575.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.029201 restraints weight = 24776.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029589 restraints weight = 19877.997| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13032 Z= 0.109 Angle : 0.576 8.572 17769 Z= 0.278 Chirality : 0.042 0.210 2034 Planarity : 0.004 0.049 2220 Dihedral : 6.205 52.647 2337 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1557 helix: 0.73 (0.38), residues: 204 sheet: -1.59 (0.22), residues: 501 loop : -1.06 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 18 TYR 0.008 0.001 TYR J 91 PHE 0.009 0.001 PHE B 234 TRP 0.013 0.001 TRP C 104 HIS 0.006 0.001 HIS F 516 Details of bonding type rmsd covalent geometry : bond 0.00243 (12987) covalent geometry : angle 0.55679 (17649) SS BOND : bond 0.00252 ( 15) SS BOND : angle 1.21857 ( 30) hydrogen bonds : bond 0.02728 ( 324) hydrogen bonds : angle 4.98723 ( 891) link_ALPHA1-2 : bond 0.00168 ( 3) link_ALPHA1-2 : angle 2.64419 ( 9) link_ALPHA1-3 : bond 0.01566 ( 3) link_ALPHA1-3 : angle 0.53957 ( 9) link_ALPHA1-6 : bond 0.00634 ( 3) link_ALPHA1-6 : angle 1.58368 ( 9) link_BETA1-4 : bond 0.00356 ( 9) link_BETA1-4 : angle 1.41430 ( 27) link_NAG-ASN : bond 0.00337 ( 12) link_NAG-ASN : angle 2.57929 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1813.57 seconds wall clock time: 32 minutes 27.39 seconds (1947.39 seconds total)