Starting phenix.real_space_refine on Sat Sep 12 01:31:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_8935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_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_8935/09_2026/6dzl_8935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_8935.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_8935.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_8935.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_8935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzl_8935/09_2026/6dzl_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-2.2.1-6174/lib/python3.11/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 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 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 chiralities: 2 Restraints were copied for chains: B, C, E, F, K, L, H, I, O, Q, P, R Time building chain proxies: 2.16, per 1000 atoms: 0.17 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: 1.20 Conformation dependent library (CDL) restraints added in 565.0 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: 0.36 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: 2.05 Time building geometry restraints manager: 1.55 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 - 10.40: 6671 10.40 - 20.80: 562 20.80 - 31.20: 90 31.20 - 41.60: 48 41.60 - 52.00: 21 Dihedral angle restraints: 7392 sinusoidal: 2856 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 7389 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: 0.03 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: 4.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 8.574 51.996 4461 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/Z covalent geometry : bond 0.01161 / 0.53 (12987) covalent geometry : angle 0.95357 / 0.50 (17649) SS BOND : bond 0.00487 / 0.31 ( 15) SS BOND : angle 1.14991 / 0.72 ( 30) hydrogen bonds : bond 0.23990 / 15.90 ( 324) hydrogen bonds : angle 11.24842 / 7.47 ( 891) link_ALPHA1-2 : bond 0.00393 / 0.20 ( 3) link_ALPHA1-2 : angle 2.56540 / 1.37 ( 9) link_ALPHA1-3 : bond 0.00271 / 0.14 ( 3) link_ALPHA1-3 : angle 3.03537 / 1.65 ( 9) link_ALPHA1-6 : bond 0.00349 / 0.18 ( 3) link_ALPHA1-6 : angle 1.79626 / 1.01 ( 9) link_BETA1-4 : bond 0.01202 / 0.96 ( 9) link_BETA1-4 : angle 2.35592 / 1.40 ( 27) link_NAG-ASN : bond 0.00423 / 0.28 ( 12) link_NAG-ASN : angle 6.76171 / 3.57 ( 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 : 0.370 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: 0.1395 time to fit residues: 44.7074 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 : 0.402 ------------------------------------------------------------------------------- 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... ** 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** 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 = 0.2963 r_free = 0.2963 target = 0.037240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030315 restraints weight = 94811.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.031451 restraints weight = 50335.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032260 restraints weight = 32786.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.032838 restraints weight = 24117.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.033255 restraints weight = 19289.594| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13032 Z= 0.153 Angle : 0.700 8.712 17769 Z= 0.345 Chirality : 0.045 0.267 2034 Planarity : 0.005 0.041 2220 Dihedral : 5.823 21.125 1731 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -2.83 (0.20), residues: 450 loop : -2.24 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.014 0.002 TYR A 261 PHE 0.017 0.001 PHE D 572 TRP 0.007 0.001 TRP E 518 HIS 0.004 0.001 HIS E 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (12987) covalent geometry : angle 0.66518 / 0.34 (17649) SS BOND : bond 0.00964 / 0.71 ( 15) SS BOND : angle 2.08583 / 1.41 ( 30) hydrogen bonds : bond 0.03648 / 2.46 ( 324) hydrogen bonds : angle 7.13801 / 4.76 ( 891) link_ALPHA1-2 : bond 0.00275 / 0.14 ( 3) link_ALPHA1-2 : angle 1.80350 / 1.01 ( 9) link_ALPHA1-3 : bond 0.00937 / 0.47 ( 3) link_ALPHA1-3 : angle 2.99075 / 1.59 ( 9) link_ALPHA1-6 : bond 0.00300 / 0.15 ( 3) link_ALPHA1-6 : angle 1.41113 / 0.80 ( 9) link_BETA1-4 : bond 0.00591 / 0.36 ( 9) link_BETA1-4 : angle 1.68729 / 0.99 ( 27) link_NAG-ASN : bond 0.00521 / 0.32 ( 12) link_NAG-ASN : angle 3.97169 / 2.13 ( 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 159 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8233 (m-30) cc_final: 0.7883 (m-30) REVERT: J 33 LEU cc_start: 0.8832 (tp) cc_final: 0.8631 (tp) REVERT: G 39 GLN cc_start: 0.9590 (tt0) cc_final: 0.9075 (tm-30) REVERT: G 51 ILE cc_start: 0.9581 (tt) cc_final: 0.9338 (tp) REVERT: E 552 ASP cc_start: 0.8484 (m-30) cc_final: 0.8102 (m-30) REVERT: K 27 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8442 (tm-30) REVERT: H 39 GLN cc_start: 0.9613 (tt0) cc_final: 0.9124 (tm-30) REVERT: H 73 ASN cc_start: 0.9242 (p0) cc_final: 0.8823 (m-40) REVERT: H 75 LYS cc_start: 0.9611 (ttmm) cc_final: 0.9349 (ttmm) REVERT: C 69 ASN cc_start: 0.8916 (m-40) cc_final: 0.8621 (m110) REVERT: L 74 THR cc_start: 0.9245 (t) cc_final: 0.8973 (t) REVERT: I 39 GLN cc_start: 0.9538 (tt0) cc_final: 0.9122 (tm-30) REVERT: I 73 ASN cc_start: 0.9093 (p0) cc_final: 0.8810 (m-40) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1327 time to fit residues: 29.5732 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 : 0.493 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 91 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.035479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028476 restraints weight = 96748.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029557 restraints weight = 52593.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.030329 restraints weight = 34905.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.030872 restraints weight = 26068.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.031288 restraints weight = 21073.993| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13032 Z= 0.185 Angle : 0.656 7.644 17769 Z= 0.320 Chirality : 0.044 0.300 2034 Planarity : 0.005 0.059 2220 Dihedral : 5.301 20.894 1731 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -2.81 (0.21), residues: 1557 helix: -0.39 (0.40), residues: 177 sheet: -2.45 (0.21), residues: 459 loop : -1.85 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 97 TYR 0.013 0.002 TYR A 261 PHE 0.009 0.001 PHE K 71 TRP 0.007 0.001 TRP E 597 HIS 0.003 0.001 HIS G 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (12987) covalent geometry : angle 0.62788 / 0.31 (17649) SS BOND : bond 0.00334 / 0.20 ( 15) SS BOND : angle 1.18392 / 0.76 ( 30) hydrogen bonds : bond 0.03446 / 2.29 ( 324) hydrogen bonds : angle 6.38266 / 4.30 ( 891) link_ALPHA1-2 : bond 0.00293 / 0.15 ( 3) link_ALPHA1-2 : angle 1.61481 / 0.89 ( 9) link_ALPHA1-3 : bond 0.00601 / 0.30 ( 3) link_ALPHA1-3 : angle 2.41089 / 1.29 ( 9) link_ALPHA1-6 : bond 0.00352 / 0.18 ( 3) link_ALPHA1-6 : angle 1.65886 / 0.94 ( 9) link_BETA1-4 : bond 0.00591 / 0.40 ( 9) link_BETA1-4 : angle 1.66273 / 0.99 ( 27) link_NAG-ASN : bond 0.00255 / 0.16 ( 12) link_NAG-ASN : angle 3.64463 / 1.94 ( 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 120 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9094 (ptpp) cc_final: 0.8863 (ptpp) REVERT: D 552 ASP cc_start: 0.8301 (m-30) cc_final: 0.7989 (m-30) REVERT: J 33 LEU cc_start: 0.8820 (tp) cc_final: 0.8544 (tp) REVERT: J 83 PHE cc_start: 0.8654 (m-80) cc_final: 0.8357 (m-80) REVERT: G 39 GLN cc_start: 0.9604 (tt0) cc_final: 0.9107 (tt0) REVERT: E 552 ASP cc_start: 0.8627 (m-30) cc_final: 0.8186 (m-30) REVERT: H 39 GLN cc_start: 0.9613 (tt0) cc_final: 0.9361 (tt0) REVERT: H 73 ASN cc_start: 0.9064 (p0) cc_final: 0.8795 (m-40) REVERT: H 75 LYS cc_start: 0.9600 (ttmm) cc_final: 0.9387 (ttmm) REVERT: H 83 ARG cc_start: 0.8646 (mtm-85) cc_final: 0.8174 (mtm180) REVERT: C 69 ASN cc_start: 0.9017 (m-40) cc_final: 0.8697 (m110) REVERT: L 83 PHE cc_start: 0.8727 (m-80) cc_final: 0.8440 (m-80) REVERT: I 39 GLN cc_start: 0.9543 (tt0) cc_final: 0.9120 (tt0) REVERT: I 83 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8432 (mtm180) REVERT: I 105 GLN cc_start: 0.8952 (mp10) cc_final: 0.8732 (mp10) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1234 time to fit residues: 21.0819 Evaluate side-chains 90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 0.9980 chunk 100 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 551 GLN G 6 GLN E 551 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.035363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.028277 restraints weight = 95524.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.029384 restraints weight = 50773.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.030170 restraints weight = 33312.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.030732 restraints weight = 24690.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.031150 restraints weight = 19840.531| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13032 Z= 0.118 Angle : 0.578 7.642 17769 Z= 0.283 Chirality : 0.042 0.263 2034 Planarity : 0.004 0.055 2220 Dihedral : 4.808 19.081 1731 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -0.09 (0.37), residues: 201 sheet: -1.99 (0.23), residues: 456 loop : -1.75 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 97 TYR 0.011 0.001 TYR A 261 PHE 0.009 0.001 PHE F 582 TRP 0.008 0.001 TRP B 104 HIS 0.005 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (12987) covalent geometry : angle 0.55127 / 0.28 (17649) SS BOND : bond 0.00350 / 0.22 ( 15) SS BOND : angle 1.29719 / 0.86 ( 30) hydrogen bonds : bond 0.02988 / 2.02 ( 324) hydrogen bonds : angle 5.76906 / 3.87 ( 891) link_ALPHA1-2 : bond 0.00382 / 0.19 ( 3) link_ALPHA1-2 : angle 1.49106 / 0.84 ( 9) link_ALPHA1-3 : bond 0.00849 / 0.43 ( 3) link_ALPHA1-3 : angle 2.42967 / 1.28 ( 9) link_ALPHA1-6 : bond 0.00383 / 0.19 ( 3) link_ALPHA1-6 : angle 1.41622 / 0.80 ( 9) link_BETA1-4 : bond 0.00365 / 0.24 ( 9) link_BETA1-4 : angle 1.47506 / 0.89 ( 27) link_NAG-ASN : bond 0.00409 / 0.25 ( 12) link_NAG-ASN : angle 3.22502 / 1.72 ( 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 121 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.466 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: D 552 ASP cc_start: 0.8239 (m-30) cc_final: 0.7957 (m-30) REVERT: J 33 LEU cc_start: 0.8955 (tp) cc_final: 0.8731 (tp) REVERT: G 39 GLN cc_start: 0.9598 (tt0) cc_final: 0.9072 (tt0) REVERT: G 83 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8268 (mtm180) REVERT: B 69 ASN cc_start: 0.9077 (m-40) cc_final: 0.8837 (m110) REVERT: E 552 ASP cc_start: 0.8527 (m-30) cc_final: 0.8043 (m-30) REVERT: K 27 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8486 (tm-30) REVERT: H 39 GLN cc_start: 0.9607 (tt0) cc_final: 0.9185 (tm-30) REVERT: H 73 ASN cc_start: 0.9040 (p0) cc_final: 0.8762 (m-40) REVERT: H 75 LYS cc_start: 0.9575 (ttmm) cc_final: 0.9352 (ttmm) REVERT: H 83 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.8303 (mtm180) REVERT: C 69 ASN cc_start: 0.9046 (m-40) cc_final: 0.8732 (m110) REVERT: F 552 ASP cc_start: 0.8486 (m-30) cc_final: 0.8062 (m-30) REVERT: I 39 GLN cc_start: 0.9547 (tt0) cc_final: 0.9135 (tm-30) REVERT: I 83 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8266 (mtm180) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1292 time to fit residues: 22.1383 Evaluate side-chains 87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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: 0.6980 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 145 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.035385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.028370 restraints weight = 94437.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.029470 restraints weight = 50238.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.030259 restraints weight = 32871.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.030807 restraints weight = 24299.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.031189 restraints weight = 19504.028| |-----------------------------------------------------------------------------| r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4070 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= 0.102 Angle : 0.556 7.238 17769 Z= 0.271 Chirality : 0.041 0.250 2034 Planarity : 0.004 0.054 2220 Dihedral : 4.544 17.649 1731 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % 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: -1.99 (0.21), residues: 1557 helix: 0.16 (0.37), residues: 201 sheet: -1.59 (0.24), residues: 447 loop : -1.52 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 19 TYR 0.010 0.001 TYR A 261 PHE 0.009 0.001 PHE J 83 TRP 0.005 0.001 TRP A 104 HIS 0.002 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (12987) covalent geometry : angle 0.53039 / 0.27 (17649) SS BOND : bond 0.00297 / 0.19 ( 15) SS BOND : angle 1.31851 / 0.85 ( 30) hydrogen bonds : bond 0.02679 / 1.81 ( 324) hydrogen bonds : angle 5.45618 / 3.65 ( 891) link_ALPHA1-2 : bond 0.00406 / 0.20 ( 3) link_ALPHA1-2 : angle 1.46956 / 0.83 ( 9) link_ALPHA1-3 : bond 0.00995 / 0.50 ( 3) link_ALPHA1-3 : angle 2.25464 / 1.19 ( 9) link_ALPHA1-6 : bond 0.00380 / 0.19 ( 3) link_ALPHA1-6 : angle 1.44126 / 0.82 ( 9) link_BETA1-4 : bond 0.00305 / 0.21 ( 9) link_BETA1-4 : angle 1.41395 / 0.84 ( 27) link_NAG-ASN : bond 0.00335 / 0.20 ( 12) link_NAG-ASN : angle 3.03904 / 1.63 ( 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 117 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.518 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: D 552 ASP cc_start: 0.8228 (m-30) cc_final: 0.7732 (m-30) REVERT: J 33 LEU cc_start: 0.8969 (tp) cc_final: 0.8754 (tp) REVERT: G 39 GLN cc_start: 0.9603 (tt0) cc_final: 0.9179 (tm-30) REVERT: G 83 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8320 (mtm180) REVERT: B 69 ASN cc_start: 0.9066 (m-40) cc_final: 0.8855 (m110) REVERT: B 260 ILE cc_start: 0.8558 (mm) cc_final: 0.8298 (tp) REVERT: E 552 ASP cc_start: 0.8514 (m-30) cc_final: 0.7958 (m-30) REVERT: H 73 ASN cc_start: 0.9022 (p0) cc_final: 0.8781 (m-40) REVERT: H 75 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9368 (ttmm) REVERT: H 83 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8247 (mtm180) REVERT: C 69 ASN cc_start: 0.9062 (m-40) cc_final: 0.8773 (m110) REVERT: F 552 ASP cc_start: 0.8363 (m-30) cc_final: 0.7958 (m-30) REVERT: I 39 GLN cc_start: 0.9537 (tt0) cc_final: 0.9156 (tm-30) REVERT: I 83 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8305 (mtm180) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1311 time to fit residues: 21.7712 Evaluate side-chains 87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 3.9990 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2844 r_free = 0.2844 target = 0.034211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.027143 restraints weight = 96078.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.028222 restraints weight = 50969.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.028982 restraints weight = 33481.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029549 restraints weight = 24872.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.029872 restraints weight = 20002.709| |-----------------------------------------------------------------------------| r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13032 Z= 0.165 Angle : 0.592 7.017 17769 Z= 0.286 Chirality : 0.042 0.251 2034 Planarity : 0.004 0.053 2220 Dihedral : 4.537 19.572 1731 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.46 (0.38), residues: 201 sheet: -1.91 (0.21), residues: 537 loop : -1.27 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 18 TYR 0.011 0.001 TYR J 91 PHE 0.011 0.001 PHE B 132 TRP 0.022 0.001 TRP C 104 HIS 0.005 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (12987) covalent geometry : angle 0.57120 / 0.28 (17649) SS BOND : bond 0.00260 / 0.17 ( 15) SS BOND : angle 0.92107 / 0.56 ( 30) hydrogen bonds : bond 0.02863 / 1.92 ( 324) hydrogen bonds : angle 5.36475 / 3.61 ( 891) link_ALPHA1-2 : bond 0.00373 / 0.19 ( 3) link_ALPHA1-2 : angle 1.66439 / 0.94 ( 9) link_ALPHA1-3 : bond 0.00596 / 0.30 ( 3) link_ALPHA1-3 : angle 1.92688 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00278 / 0.14 ( 3) link_ALPHA1-6 : angle 1.46795 / 0.83 ( 9) link_BETA1-4 : bond 0.00460 / 0.36 ( 9) link_BETA1-4 : angle 1.59039 / 0.94 ( 27) link_NAG-ASN : bond 0.00226 / 0.15 ( 12) link_NAG-ASN : angle 2.87633 / 1.56 ( 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 106 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.468 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: A 140 LYS cc_start: 0.9293 (ptpp) cc_final: 0.8998 (ptpp) REVERT: D 552 ASP cc_start: 0.8455 (m-30) cc_final: 0.7962 (m-30) REVERT: J 33 LEU cc_start: 0.9000 (tp) cc_final: 0.8786 (tp) REVERT: G 39 GLN cc_start: 0.9619 (tt0) cc_final: 0.9201 (tm-30) REVERT: G 83 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8405 (mtm180) REVERT: B 69 ASN cc_start: 0.9135 (m-40) cc_final: 0.8823 (m110) REVERT: B 260 ILE cc_start: 0.8645 (mm) cc_final: 0.8330 (tp) REVERT: E 552 ASP cc_start: 0.8653 (m-30) cc_final: 0.8123 (m-30) REVERT: H 73 ASN cc_start: 0.9044 (p0) cc_final: 0.8755 (m-40) REVERT: H 75 LYS cc_start: 0.9593 (ttmm) cc_final: 0.9354 (ttmm) REVERT: H 83 ARG cc_start: 0.8784 (mtm-85) cc_final: 0.8337 (mtm180) REVERT: C 69 ASN cc_start: 0.9118 (m-40) cc_final: 0.8688 (m110) REVERT: C 260 ILE cc_start: 0.8516 (mm) cc_final: 0.8287 (tp) REVERT: F 552 ASP cc_start: 0.8617 (m-30) cc_final: 0.8139 (m-30) REVERT: I 83 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8369 (mtm180) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1537 time to fit residues: 22.0998 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: 0.2980 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2861 r_free = 0.2861 target = 0.034601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.027566 restraints weight = 97662.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.028639 restraints weight = 53667.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.029409 restraints weight = 35763.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.029969 restraints weight = 26765.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.030355 restraints weight = 21524.088| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13032 Z= 0.123 Angle : 0.547 7.647 17769 Z= 0.266 Chirality : 0.041 0.237 2034 Planarity : 0.004 0.052 2220 Dihedral : 4.423 19.442 1731 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % 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: -1.73 (0.22), residues: 1557 helix: 0.72 (0.39), residues: 201 sheet: -1.59 (0.22), residues: 519 loop : -1.27 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.009 0.001 TYR C 261 PHE 0.010 0.001 PHE B 234 TRP 0.013 0.001 TRP C 104 HIS 0.012 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (12987) covalent geometry : angle 0.52727 / 0.26 (17649) SS BOND : bond 0.00234 / 0.15 ( 15) SS BOND : angle 0.74220 / 0.46 ( 30) hydrogen bonds : bond 0.02640 / 1.78 ( 324) hydrogen bonds : angle 5.15051 / 3.45 ( 891) link_ALPHA1-2 : bond 0.00175 / 0.09 ( 3) link_ALPHA1-2 : angle 1.65952 / 0.93 ( 9) link_ALPHA1-3 : bond 0.00775 / 0.39 ( 3) link_ALPHA1-3 : angle 1.88094 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00331 / 0.17 ( 3) link_ALPHA1-6 : angle 1.44073 / 0.81 ( 9) link_BETA1-4 : bond 0.00315 / 0.23 ( 9) link_BETA1-4 : angle 1.40784 / 0.86 ( 27) link_NAG-ASN : bond 0.00293 / 0.18 ( 12) link_NAG-ASN : angle 2.70473 / 1.44 ( 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 106 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9285 (ptpp) cc_final: 0.8979 (ptpp) REVERT: D 552 ASP cc_start: 0.8303 (m-30) cc_final: 0.7860 (m-30) REVERT: D 574 ARG cc_start: 0.9409 (ttt180) cc_final: 0.9115 (ttt180) REVERT: J 33 LEU cc_start: 0.9005 (tp) cc_final: 0.8787 (tp) REVERT: G 39 GLN cc_start: 0.9588 (tt0) cc_final: 0.9219 (tm-30) REVERT: G 83 ARG cc_start: 0.8757 (mtm-85) cc_final: 0.8405 (mtm180) REVERT: B 69 ASN cc_start: 0.9125 (m-40) cc_final: 0.8870 (m110) REVERT: B 260 ILE cc_start: 0.8609 (mm) cc_final: 0.8331 (tp) REVERT: E 552 ASP cc_start: 0.8538 (m-30) cc_final: 0.8034 (m-30) REVERT: K 75 ILE cc_start: 0.9166 (mp) cc_final: 0.8950 (pt) REVERT: H 75 LYS cc_start: 0.9578 (ttmm) cc_final: 0.9331 (ttmm) REVERT: H 83 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8431 (mtm180) REVERT: C 69 ASN cc_start: 0.9047 (m-40) cc_final: 0.8677 (m110) REVERT: C 260 ILE cc_start: 0.8470 (mm) cc_final: 0.8264 (tp) REVERT: F 552 ASP cc_start: 0.8414 (m-30) cc_final: 0.7934 (m-30) REVERT: I 83 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8347 (mtm180) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1364 time to fit residues: 20.1412 Evaluate side-chains 81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 6.9990 chunk 105 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2806 r_free = 0.2806 target = 0.033085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026211 restraints weight = 99686.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.027222 restraints weight = 54927.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.027964 restraints weight = 36794.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.028486 restraints weight = 27527.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.028810 restraints weight = 22310.012| |-----------------------------------------------------------------------------| r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13032 Z= 0.231 Angle : 0.643 7.130 17769 Z= 0.309 Chirality : 0.042 0.265 2034 Planarity : 0.004 0.049 2220 Dihedral : 4.675 22.690 1731 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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: -1.77 (0.22), residues: 1557 helix: 0.76 (0.38), residues: 201 sheet: -1.85 (0.21), residues: 519 loop : -1.12 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 18 TYR 0.015 0.002 TYR H 90 PHE 0.017 0.002 PHE K 71 TRP 0.014 0.002 TRP H 99 HIS 0.011 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.23 (12987) covalent geometry : angle 0.62550 / 0.31 (17649) SS BOND : bond 0.00257 / 0.17 ( 15) SS BOND : angle 0.76641 / 0.47 ( 30) hydrogen bonds : bond 0.03154 / 2.13 ( 324) hydrogen bonds : angle 5.37226 / 3.64 ( 891) link_ALPHA1-2 : bond 0.00031 / 0.02 ( 3) link_ALPHA1-2 : angle 1.73599 / 0.98 ( 9) link_ALPHA1-3 : bond 0.00375 / 0.19 ( 3) link_ALPHA1-3 : angle 1.62700 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00182 / 0.09 ( 3) link_ALPHA1-6 : angle 1.53643 / 0.87 ( 9) link_BETA1-4 : bond 0.00586 / 0.45 ( 9) link_BETA1-4 : angle 1.77464 / 1.05 ( 27) link_NAG-ASN : bond 0.00327 / 0.22 ( 12) link_NAG-ASN : angle 2.69820 / 1.47 ( 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 101 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.535 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: A 140 LYS cc_start: 0.9313 (ptpp) cc_final: 0.8927 (ptpp) REVERT: D 552 ASP cc_start: 0.8329 (m-30) cc_final: 0.7908 (m-30) REVERT: J 33 LEU cc_start: 0.9088 (tp) cc_final: 0.8877 (tp) REVERT: G 83 ARG cc_start: 0.8801 (mtm-85) cc_final: 0.8428 (mtm180) REVERT: B 260 ILE cc_start: 0.8625 (mm) cc_final: 0.8381 (tp) REVERT: E 552 ASP cc_start: 0.8515 (m-30) cc_final: 0.8043 (m-30) REVERT: H 75 LYS cc_start: 0.9539 (ttmm) cc_final: 0.9270 (ttmm) REVERT: H 83 ARG cc_start: 0.8849 (mtm-85) cc_final: 0.8492 (mtm180) REVERT: C 260 ILE cc_start: 0.8508 (mm) cc_final: 0.8306 (tp) REVERT: F 552 ASP cc_start: 0.8568 (m-30) cc_final: 0.8058 (m-30) REVERT: I 83 ARG cc_start: 0.8791 (mtm-85) cc_final: 0.8401 (mtm180) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1502 time to fit residues: 21.1392 Evaluate side-chains 74 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 570 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.033667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.026747 restraints weight = 97382.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.027798 restraints weight = 53408.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.028560 restraints weight = 35713.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.029097 restraints weight = 26524.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.029511 restraints weight = 21362.627| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13032 Z= 0.136 Angle : 0.567 8.127 17769 Z= 0.276 Chirality : 0.042 0.287 2034 Planarity : 0.004 0.050 2220 Dihedral : 4.564 21.486 1731 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % 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: -1.57 (0.22), residues: 1557 helix: 0.78 (0.39), residues: 201 sheet: -1.50 (0.23), residues: 456 loop : -1.19 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 18 TYR 0.009 0.001 TYR J 91 PHE 0.008 0.001 PHE K 83 TRP 0.013 0.001 TRP C 104 HIS 0.009 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (12987) covalent geometry : angle 0.54906 / 0.27 (17649) SS BOND : bond 0.00513 / 0.38 ( 15) SS BOND : angle 1.29137 / 0.93 ( 30) hydrogen bonds : bond 0.02881 / 1.94 ( 324) hydrogen bonds : angle 5.19622 / 3.50 ( 891) link_ALPHA1-2 : bond 0.00065 / 0.03 ( 3) link_ALPHA1-2 : angle 1.76981 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00675 / 0.34 ( 3) link_ALPHA1-3 : angle 1.68013 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00297 / 0.15 ( 3) link_ALPHA1-6 : angle 1.44028 / 0.81 ( 9) link_BETA1-4 : bond 0.00341 / 0.24 ( 9) link_BETA1-4 : angle 1.40251 / 0.88 ( 27) link_NAG-ASN : bond 0.00287 / 0.18 ( 12) link_NAG-ASN : angle 2.50589 / 1.34 ( 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 98 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 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: A 140 LYS cc_start: 0.9295 (ptpp) cc_final: 0.8901 (ptpp) REVERT: D 552 ASP cc_start: 0.8295 (m-30) cc_final: 0.7857 (m-30) REVERT: D 555 ILE cc_start: 0.9601 (mp) cc_final: 0.9016 (tt) REVERT: G 83 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.8540 (mtm180) REVERT: B 260 ILE cc_start: 0.8598 (mm) cc_final: 0.8361 (tp) REVERT: E 552 ASP cc_start: 0.8499 (m-30) cc_final: 0.8036 (m-30) REVERT: H 34 MET cc_start: 0.9375 (mmp) cc_final: 0.9096 (mmp) REVERT: H 75 LYS cc_start: 0.9547 (ttmm) cc_final: 0.9276 (ttmm) REVERT: C 69 ASN cc_start: 0.9081 (m-40) cc_final: 0.8630 (m110) REVERT: C 260 ILE cc_start: 0.8633 (mm) cc_final: 0.8396 (tp) REVERT: F 552 ASP cc_start: 0.8460 (m-30) cc_final: 0.8035 (m-30) REVERT: I 83 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8476 (mtm180) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1405 time to fit residues: 19.5729 Evaluate side-chains 67 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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: 3.9990 chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 73 ASN ** 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 = 0.032793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.025944 restraints weight = 99985.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.026949 restraints weight = 54844.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.027676 restraints weight = 36753.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028173 restraints weight = 27532.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.028515 restraints weight = 22309.060| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13032 Z= 0.244 Angle : 0.654 7.427 17769 Z= 0.316 Chirality : 0.043 0.259 2034 Planarity : 0.004 0.047 2220 Dihedral : 4.807 24.180 1731 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % 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: -1.73 (0.22), residues: 1557 helix: 0.63 (0.39), residues: 201 sheet: -1.73 (0.21), residues: 513 loop : -1.13 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 83 TYR 0.014 0.002 TYR H 90 PHE 0.015 0.002 PHE K 71 TRP 0.015 0.002 TRP I 99 HIS 0.012 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (12987) covalent geometry : angle 0.63837 / 0.31 (17649) SS BOND : bond 0.00218 / 0.15 ( 15) SS BOND : angle 1.00049 / 0.70 ( 30) hydrogen bonds : bond 0.03249 / 2.21 ( 324) hydrogen bonds : angle 5.35391 / 3.63 ( 891) link_ALPHA1-2 : bond 0.00091 / 0.05 ( 3) link_ALPHA1-2 : angle 1.76194 / 0.99 ( 9) link_ALPHA1-3 : bond 0.00465 / 0.23 ( 3) link_ALPHA1-3 : angle 1.52563 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00142 / 0.07 ( 3) link_ALPHA1-6 : angle 1.53545 / 0.87 ( 9) link_BETA1-4 : bond 0.00593 / 0.46 ( 9) link_BETA1-4 : angle 1.67474 / 1.01 ( 27) link_NAG-ASN : bond 0.00318 / 0.21 ( 12) link_NAG-ASN : angle 2.55917 / 1.39 ( 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 86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.647 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: A 140 LYS cc_start: 0.9334 (ptpp) cc_final: 0.8926 (ptpp) REVERT: D 552 ASP cc_start: 0.8433 (m-30) cc_final: 0.8040 (m-30) REVERT: D 555 ILE cc_start: 0.9640 (mp) cc_final: 0.9123 (tt) REVERT: B 260 ILE cc_start: 0.8657 (mm) cc_final: 0.8416 (tp) REVERT: E 552 ASP cc_start: 0.8593 (m-30) cc_final: 0.8168 (m-30) REVERT: H 75 LYS cc_start: 0.9489 (ttmm) cc_final: 0.9221 (ttmm) REVERT: C 260 ILE cc_start: 0.8609 (mm) cc_final: 0.8407 (tp) REVERT: F 552 ASP cc_start: 0.8544 (m-30) cc_final: 0.8131 (m-30) REVERT: I 83 ARG cc_start: 0.8838 (mtm-85) cc_final: 0.8517 (mtm180) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1390 time to fit residues: 17.1697 Evaluate side-chains 69 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.6980 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 152 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.2824 r_free = 0.2824 target = 0.033620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.026784 restraints weight = 96597.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.027835 restraints weight = 52609.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.028593 restraints weight = 35000.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.029124 restraints weight = 25831.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.029527 restraints weight = 20715.589| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13032 Z= 0.118 Angle : 0.567 8.958 17769 Z= 0.275 Chirality : 0.041 0.220 2034 Planarity : 0.004 0.049 2220 Dihedral : 4.563 21.979 1731 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: -1.53 (0.22), residues: 1557 helix: 0.65 (0.38), residues: 204 sheet: -1.43 (0.22), residues: 486 loop : -1.12 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 18 TYR 0.009 0.001 TYR J 91 PHE 0.008 0.001 PHE D 582 TRP 0.015 0.001 TRP C 104 HIS 0.008 0.001 HIS F 516 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (12987) covalent geometry : angle 0.55108 / 0.27 (17649) SS BOND : bond 0.00200 / 0.12 ( 15) SS BOND : angle 1.00998 / 0.71 ( 30) hydrogen bonds : bond 0.02840 / 1.93 ( 324) hydrogen bonds : angle 5.11472 / 3.43 ( 891) link_ALPHA1-2 : bond 0.00070 / 0.04 ( 3) link_ALPHA1-2 : angle 1.84653 / 1.01 ( 9) link_ALPHA1-3 : bond 0.00757 / 0.38 ( 3) link_ALPHA1-3 : angle 1.56446 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00306 / 0.15 ( 3) link_ALPHA1-6 : angle 1.41636 / 0.80 ( 9) link_BETA1-4 : bond 0.00326 / 0.22 ( 9) link_BETA1-4 : angle 1.31496 / 0.84 ( 27) link_NAG-ASN : bond 0.00334 / 0.20 ( 12) link_NAG-ASN : angle 2.40276 / 1.29 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.59 seconds wall clock time: 32 minutes 31.25 seconds (1951.25 seconds total)