Starting phenix.real_space_refine on Wed Jul 30 23:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.map" model { file = "/net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dzl_8935/07_2025/6dzl_8935.cif" } resolution = 4.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: "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: "E" 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: "K" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: I, H, D, F, O, Q, P, R, C, B, J, L Time building chain proxies: 7.03, per 1000 atoms: 0.55 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=6, 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 C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.04 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: 3.52 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.60 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: 3.43 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4020 1.34 - 1.46: 3431 1.46 - 1.58: 5485 1.58 - 1.70: 0 1.70 - 1.82: 51 Bond restraints: 12987 Sorted by residual: bond pdb=" C PHE A 132 " pdb=" N PRO A 133 " ideal model delta sigma weight residual 1.336 1.309 0.026 1.23e-02 6.61e+03 4.64e+00 bond pdb=" C PHE C 132 " pdb=" N PRO C 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.12e+00 bond pdb=" C PHE B 132 " pdb=" N PRO B 133 " ideal model delta sigma weight residual 1.336 1.311 0.025 1.23e-02 6.61e+03 4.08e+00 bond pdb=" CA ARG C 134 " pdb=" CB ARG C 134 " ideal model delta sigma weight residual 1.527 1.480 0.047 2.48e-02 1.63e+03 3.61e+00 bond pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta sigma weight residual 1.533 1.490 0.043 2.29e-02 1.91e+03 3.49e+00 ... (remaining 12982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16447 1.73 - 3.45: 1013 3.45 - 5.18: 159 5.18 - 6.90: 21 6.90 - 8.63: 9 Bond angle restraints: 17649 Sorted by residual: angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.10 109.66 4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" N ALA L 51 " pdb=" CA ALA L 51 " pdb=" CB ALA L 51 " ideal model delta sigma weight residual 114.10 109.73 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" N ALA J 51 " pdb=" CA ALA J 51 " pdb=" CB ALA J 51 " ideal model delta sigma weight residual 114.10 109.75 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" N GLY D 524 " pdb=" CA GLY D 524 " pdb=" C GLY D 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 angle pdb=" N GLY F 524 " pdb=" CA GLY F 524 " pdb=" C GLY F 524 " ideal model delta sigma weight residual 113.18 104.55 8.63 2.37e+00 1.78e-01 1.33e+01 ... (remaining 17644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.65: 7761 22.65 - 45.29: 174 45.29 - 67.94: 6 67.94 - 90.58: 18 90.58 - 113.23: 12 Dihedral angle restraints: 7971 sinusoidal: 3435 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 7968 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: 2.03 - 2.61: 225 2.61 - 3.18: 12108 3.18 - 3.75: 19334 3.75 - 4.33: 27419 4.33 - 4.90: 44387 Nonbonded interactions: 103473 Sorted by model distance: nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS G 22 " pdb=" SG CYS G 92 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.035 3.760 nonbonded pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " model vdw 2.035 3.760 ... (remaining 103468 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: 0.08 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } ncs_group { reference = chain 'K' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.860 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.073 13023 Z= 0.533 Angle : 1.008 12.220 17751 Z= 0.512 Chirality : 0.080 1.585 2034 Planarity : 0.006 0.050 2220 Dihedral : 11.385 113.229 5067 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (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 TRP 0.019 0.003 TRP G 47 HIS 0.004 0.001 HIS I 100D PHE 0.017 0.003 PHE K 71 TYR 0.017 0.003 TYR A 109 ARG 0.010 0.001 ARG F 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 6.76171 ( 36) link_ALPHA1-6 : bond 0.00349 ( 3) link_ALPHA1-6 : angle 1.79626 ( 9) link_BETA1-4 : bond 0.01202 ( 9) link_BETA1-4 : angle 2.35592 ( 27) link_ALPHA1-2 : bond 0.00393 ( 3) link_ALPHA1-2 : angle 2.56540 ( 9) link_ALPHA1-3 : bond 0.00271 ( 3) link_ALPHA1-3 : angle 3.03537 ( 9) hydrogen bonds : bond 0.23990 ( 324) hydrogen bonds : angle 11.24842 ( 891) SS BOND : bond 0.00499 ( 6) SS BOND : angle 1.46170 ( 12) covalent geometry : bond 0.01161 (12987) covalent geometry : angle 0.95357 (17649) *********************** 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 : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.9237 (tt0) REVERT: H 39 GLN cc_start: 0.9558 (tt0) cc_final: 0.9249 (tt0) REVERT: C 84 LYS cc_start: 0.9776 (mttt) cc_final: 0.9551 (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: 0.3308 time to fit residues: 105.4555 Evaluate side-chains 94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN G 13 GLN ** E 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 13 GLN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN I 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030349 restraints weight = 97355.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.031455 restraints weight = 51900.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.032244 restraints weight = 34133.728| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13023 Z= 0.154 Angle : 0.695 8.672 17751 Z= 0.343 Chirality : 0.046 0.319 2034 Planarity : 0.005 0.041 2220 Dihedral : 9.963 75.994 2337 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.20), residues: 1557 helix: -0.75 (0.40), residues: 177 sheet: -2.79 (0.20), residues: 435 loop : -2.20 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 597 HIS 0.005 0.001 HIS E 549 PHE 0.017 0.001 PHE D 572 TYR 0.014 0.002 TYR A 261 ARG 0.006 0.001 ARG A 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 12) link_NAG-ASN : angle 4.12254 ( 36) link_ALPHA1-6 : bond 0.00245 ( 3) link_ALPHA1-6 : angle 2.10299 ( 9) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 1.88569 ( 27) link_ALPHA1-2 : bond 0.00428 ( 3) link_ALPHA1-2 : angle 1.56024 ( 9) link_ALPHA1-3 : bond 0.01447 ( 3) link_ALPHA1-3 : angle 2.25231 ( 9) hydrogen bonds : bond 0.03900 ( 324) hydrogen bonds : angle 7.16573 ( 891) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.71373 ( 12) covalent geometry : bond 0.00330 (12987) covalent geometry : angle 0.66277 (17649) *********************** 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 163 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8331 (m-30) cc_final: 0.7973 (m-30) REVERT: J 33 LEU cc_start: 0.8900 (tp) cc_final: 0.8587 (tp) REVERT: G 51 ILE cc_start: 0.9578 (tt) cc_final: 0.9340 (tp) REVERT: E 552 ASP cc_start: 0.8560 (m-30) cc_final: 0.8161 (m-30) REVERT: K 27 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8435 (tm-30) REVERT: H 39 GLN cc_start: 0.9613 (tt0) cc_final: 0.9102 (tm-30) REVERT: H 73 ASN cc_start: 0.9252 (p0) cc_final: 0.8848 (m-40) REVERT: H 75 LYS cc_start: 0.9605 (ttmm) cc_final: 0.9351 (ttmm) REVERT: C 69 ASN cc_start: 0.8946 (m-40) cc_final: 0.8648 (m110) REVERT: L 74 THR cc_start: 0.9329 (t) cc_final: 0.9027 (t) REVERT: I 39 GLN cc_start: 0.9550 (tt0) cc_final: 0.9118 (tm-30) REVERT: I 73 ASN cc_start: 0.9096 (p0) cc_final: 0.8816 (m-40) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2954 time to fit residues: 65.9107 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 : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 51 optimal weight: 6.9990 chunk 53 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 140 optimal weight: 0.0970 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN K 38 GLN H 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.027843 restraints weight = 100698.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.028867 restraints weight = 55145.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.029593 restraints weight = 36979.724| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13023 Z= 0.223 Angle : 0.691 7.378 17751 Z= 0.334 Chirality : 0.045 0.334 2034 Planarity : 0.005 0.055 2220 Dihedral : 9.183 68.992 2337 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.08 % Allowed : 1.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1557 helix: -0.16 (0.40), residues: 180 sheet: -2.50 (0.21), residues: 459 loop : -1.83 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 531 HIS 0.003 0.001 HIS G 96 PHE 0.011 0.002 PHE K 71 TYR 0.014 0.002 TYR A 261 ARG 0.003 0.001 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 3.73192 ( 36) link_ALPHA1-6 : bond 0.00065 ( 3) link_ALPHA1-6 : angle 2.14090 ( 9) link_BETA1-4 : bond 0.00729 ( 9) link_BETA1-4 : angle 1.94029 ( 27) link_ALPHA1-2 : bond 0.00167 ( 3) link_ALPHA1-2 : angle 1.64792 ( 9) link_ALPHA1-3 : bond 0.01278 ( 3) link_ALPHA1-3 : angle 1.26558 ( 9) hydrogen bonds : bond 0.03702 ( 324) hydrogen bonds : angle 6.42190 ( 891) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.76310 ( 12) covalent geometry : bond 0.00474 (12987) covalent geometry : angle 0.66438 (17649) *********************** 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 119 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 1.316 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: 0.9114 (ptpp) cc_final: 0.8883 (ptpp) REVERT: D 552 ASP cc_start: 0.8480 (m-30) cc_final: 0.8041 (m-30) REVERT: J 33 LEU cc_start: 0.9065 (tp) cc_final: 0.8726 (tp) REVERT: J 74 THR cc_start: 0.9250 (t) cc_final: 0.9026 (t) REVERT: J 83 PHE cc_start: 0.8659 (m-80) cc_final: 0.8361 (m-80) REVERT: G 39 GLN cc_start: 0.9581 (tt0) cc_final: 0.9126 (tt0) REVERT: E 552 ASP cc_start: 0.8636 (m-30) cc_final: 0.8103 (m-30) REVERT: H 73 ASN cc_start: 0.9066 (p0) cc_final: 0.8829 (m-40) REVERT: H 75 LYS cc_start: 0.9554 (ttmm) cc_final: 0.9341 (ttmm) REVERT: C 69 ASN cc_start: 0.9029 (m-40) cc_final: 0.8733 (m110) REVERT: L 83 PHE cc_start: 0.8708 (m-80) cc_final: 0.8403 (m-80) REVERT: I 39 GLN cc_start: 0.9523 (tt0) cc_final: 0.9095 (tt0) REVERT: I 83 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8459 (mtm180) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.3017 time to fit residues: 49.5930 Evaluate side-chains 89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 GLN E 551 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.035030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.028123 restraints weight = 96916.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.029167 restraints weight = 52158.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.029901 restraints weight = 34638.814| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13023 Z= 0.118 Angle : 0.583 7.549 17751 Z= 0.285 Chirality : 0.043 0.270 2034 Planarity : 0.004 0.057 2220 Dihedral : 8.181 58.780 2337 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.21), residues: 1557 helix: -0.18 (0.39), residues: 177 sheet: -2.15 (0.22), residues: 471 loop : -1.65 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 531 HIS 0.003 0.001 HIS I 100D PHE 0.009 0.001 PHE F 582 TYR 0.011 0.001 TYR A 261 ARG 0.004 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 12) link_NAG-ASN : angle 3.37762 ( 36) link_ALPHA1-6 : bond 0.00368 ( 3) link_ALPHA1-6 : angle 2.07466 ( 9) link_BETA1-4 : bond 0.00375 ( 9) link_BETA1-4 : angle 1.47607 ( 27) link_ALPHA1-2 : bond 0.00288 ( 3) link_ALPHA1-2 : angle 1.77066 ( 9) link_ALPHA1-3 : bond 0.01656 ( 3) link_ALPHA1-3 : angle 1.22726 ( 9) hydrogen bonds : bond 0.03117 ( 324) hydrogen bonds : angle 5.78613 ( 891) SS BOND : bond 0.00275 ( 6) SS BOND : angle 0.46811 ( 12) covalent geometry : bond 0.00256 (12987) covalent geometry : angle 0.55747 (17649) *********************** 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 124 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8823 (ptpp) REVERT: D 552 ASP cc_start: 0.8433 (m-30) cc_final: 0.7911 (m-30) REVERT: J 33 LEU cc_start: 0.9085 (tp) cc_final: 0.8737 (tp) REVERT: G 39 GLN cc_start: 0.9600 (tt0) cc_final: 0.9098 (tt0) REVERT: G 83 ARG cc_start: 0.8725 (mtm-85) cc_final: 0.8316 (mtm180) REVERT: B 69 ASN cc_start: 0.9070 (m-40) cc_final: 0.8849 (m110) REVERT: B 140 LYS cc_start: 0.9580 (ttpt) cc_final: 0.9366 (tppt) REVERT: E 552 ASP cc_start: 0.8604 (m-30) cc_final: 0.7957 (m-30) REVERT: K 27 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8522 (tm-30) REVERT: H 73 ASN cc_start: 0.9002 (p0) cc_final: 0.8756 (m-40) REVERT: H 75 LYS cc_start: 0.9570 (ttmm) cc_final: 0.9336 (ttmm) REVERT: H 82 MET cc_start: 0.9026 (mpp) cc_final: 0.8797 (mpp) REVERT: C 69 ASN cc_start: 0.9034 (m-40) cc_final: 0.8749 (m110) REVERT: F 552 ASP cc_start: 0.8426 (m-30) cc_final: 0.7720 (m-30) REVERT: I 39 GLN cc_start: 0.9545 (tt0) cc_final: 0.9135 (tm-30) REVERT: I 83 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8334 (mtm180) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.3009 time to fit residues: 52.0048 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 : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 41 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN B 221 GLN I 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.033708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.026749 restraints weight = 100545.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.027749 restraints weight = 55201.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.028458 restraints weight = 37181.184| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13023 Z= 0.179 Angle : 0.615 6.768 17751 Z= 0.297 Chirality : 0.044 0.281 2034 Planarity : 0.004 0.054 2220 Dihedral : 7.668 54.005 2337 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1557 helix: -0.00 (0.36), residues: 201 sheet: -2.29 (0.21), residues: 504 loop : -1.38 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 531 HIS 0.003 0.001 HIS I 100D PHE 0.011 0.001 PHE B 132 TYR 0.012 0.001 TYR H 90 ARG 0.003 0.000 ARG H 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 12) link_NAG-ASN : angle 3.20947 ( 36) link_ALPHA1-6 : bond 0.00247 ( 3) link_ALPHA1-6 : angle 2.11253 ( 9) link_BETA1-4 : bond 0.00434 ( 9) link_BETA1-4 : angle 1.69827 ( 27) link_ALPHA1-2 : bond 0.00163 ( 3) link_ALPHA1-2 : angle 1.89833 ( 9) link_ALPHA1-3 : bond 0.01412 ( 3) link_ALPHA1-3 : angle 0.93289 ( 9) hydrogen bonds : bond 0.03088 ( 324) hydrogen bonds : angle 5.60339 ( 891) SS BOND : bond 0.00221 ( 6) SS BOND : angle 0.77979 ( 12) covalent geometry : bond 0.00384 (12987) covalent geometry : angle 0.59189 (17649) *********************** 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 104 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.322 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: 0.9065 (ptpp) cc_final: 0.8785 (ptpp) REVERT: D 552 ASP cc_start: 0.8606 (m-30) cc_final: 0.8165 (m-30) REVERT: J 33 LEU cc_start: 0.9151 (tp) cc_final: 0.8769 (tp) REVERT: G 39 GLN cc_start: 0.9598 (tt0) cc_final: 0.9193 (tm-30) REVERT: G 83 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8363 (mtm180) REVERT: B 69 ASN cc_start: 0.9135 (m-40) cc_final: 0.8880 (m110) REVERT: B 140 LYS cc_start: 0.9591 (ttpt) cc_final: 0.9350 (tppt) REVERT: B 260 ILE cc_start: 0.8588 (mm) cc_final: 0.8332 (tp) REVERT: E 552 ASP cc_start: 0.8745 (m-30) cc_final: 0.8234 (m-30) REVERT: H 73 ASN cc_start: 0.9030 (p0) cc_final: 0.8784 (m-40) REVERT: H 75 LYS cc_start: 0.9579 (ttmm) cc_final: 0.9340 (ttmm) REVERT: C 69 ASN cc_start: 0.9111 (m-40) cc_final: 0.8714 (m110) REVERT: F 552 ASP cc_start: 0.8555 (m-30) cc_final: 0.7856 (m-30) REVERT: I 83 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8373 (mtm180) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3203 time to fit residues: 45.5880 Evaluate side-chains 79 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.032831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.025877 restraints weight = 101962.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.026851 restraints weight = 55174.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.027556 restraints weight = 37145.548| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13023 Z= 0.201 Angle : 0.638 7.213 17751 Z= 0.306 Chirality : 0.044 0.257 2034 Planarity : 0.004 0.055 2220 Dihedral : 7.431 59.740 2337 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.22), residues: 1557 helix: 0.41 (0.38), residues: 201 sheet: -2.09 (0.20), residues: 552 loop : -1.28 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 99 HIS 0.004 0.001 HIS H 100D PHE 0.014 0.002 PHE J 83 TYR 0.014 0.002 TYR H 90 ARG 0.008 0.000 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 12) link_NAG-ASN : angle 3.02133 ( 36) link_ALPHA1-6 : bond 0.00304 ( 3) link_ALPHA1-6 : angle 2.11898 ( 9) link_BETA1-4 : bond 0.00536 ( 9) link_BETA1-4 : angle 1.58914 ( 27) link_ALPHA1-2 : bond 0.00024 ( 3) link_ALPHA1-2 : angle 2.11857 ( 9) link_ALPHA1-3 : bond 0.01395 ( 3) link_ALPHA1-3 : angle 0.82416 ( 9) hydrogen bonds : bond 0.03128 ( 324) hydrogen bonds : angle 5.45119 ( 891) SS BOND : bond 0.00924 ( 6) SS BOND : angle 1.13013 ( 12) covalent geometry : bond 0.00425 (12987) covalent geometry : angle 0.61688 (17649) *********************** 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 103 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.370 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: A 140 LYS cc_start: 0.9101 (ptpp) cc_final: 0.8789 (ptpp) REVERT: D 552 ASP cc_start: 0.8578 (m-30) cc_final: 0.8109 (m-30) REVERT: J 33 LEU cc_start: 0.9194 (tp) cc_final: 0.8866 (tp) REVERT: G 83 ARG cc_start: 0.8836 (mtm-85) cc_final: 0.8428 (mtm180) REVERT: B 69 ASN cc_start: 0.9125 (m-40) cc_final: 0.8766 (m110) REVERT: B 115 LYS cc_start: 0.9761 (mmtt) cc_final: 0.9414 (mmmt) REVERT: B 260 ILE cc_start: 0.8669 (mm) cc_final: 0.8369 (tp) REVERT: E 552 ASP cc_start: 0.8770 (m-30) cc_final: 0.8257 (m-30) REVERT: H 73 ASN cc_start: 0.9134 (p0) cc_final: 0.8843 (m-40) REVERT: H 75 LYS cc_start: 0.9587 (ttmm) cc_final: 0.9332 (ttmm) REVERT: C 69 ASN cc_start: 0.9170 (m-40) cc_final: 0.8746 (m110) REVERT: C 260 ILE cc_start: 0.8558 (mm) cc_final: 0.8307 (tp) REVERT: F 552 ASP cc_start: 0.8540 (m-30) cc_final: 0.8025 (m-30) REVERT: I 83 ARG cc_start: 0.8827 (mtm-85) cc_final: 0.8444 (mtm180) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3292 time to fit residues: 46.2350 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 : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 135 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.033331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.026374 restraints weight = 99399.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.027355 restraints weight = 54292.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028059 restraints weight = 36689.234| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13023 Z= 0.133 Angle : 0.575 7.670 17751 Z= 0.276 Chirality : 0.043 0.245 2034 Planarity : 0.004 0.053 2220 Dihedral : 7.050 59.215 2337 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.22), residues: 1557 helix: 0.63 (0.38), residues: 201 sheet: -1.81 (0.21), residues: 531 loop : -1.21 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS I 96 PHE 0.008 0.001 PHE A 234 TYR 0.011 0.001 TYR J 87 ARG 0.006 0.000 ARG K 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 12) link_NAG-ASN : angle 2.94656 ( 36) link_ALPHA1-6 : bond 0.00427 ( 3) link_ALPHA1-6 : angle 2.00162 ( 9) link_BETA1-4 : bond 0.00384 ( 9) link_BETA1-4 : angle 1.46061 ( 27) link_ALPHA1-2 : bond 0.00107 ( 3) link_ALPHA1-2 : angle 2.32957 ( 9) link_ALPHA1-3 : bond 0.01587 ( 3) link_ALPHA1-3 : angle 0.71602 ( 9) hydrogen bonds : bond 0.02870 ( 324) hydrogen bonds : angle 5.27701 ( 891) SS BOND : bond 0.00182 ( 6) SS BOND : angle 1.53810 ( 12) covalent geometry : bond 0.00293 (12987) covalent geometry : angle 0.55196 (17649) *********************** 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 102 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.332 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: D 552 ASP cc_start: 0.8521 (m-30) cc_final: 0.8035 (m-30) REVERT: J 33 LEU cc_start: 0.9203 (tp) cc_final: 0.8878 (tp) REVERT: G 83 ARG cc_start: 0.8882 (mtm-85) cc_final: 0.8599 (mtm180) REVERT: B 69 ASN cc_start: 0.9087 (m-40) cc_final: 0.8778 (m110) REVERT: B 260 ILE cc_start: 0.8620 (mm) cc_final: 0.8389 (tp) REVERT: E 552 ASP cc_start: 0.8713 (m-30) cc_final: 0.8214 (m-30) REVERT: K 75 ILE cc_start: 0.9197 (mp) cc_final: 0.8993 (pt) REVERT: H 75 LYS cc_start: 0.9591 (ttmm) cc_final: 0.9330 (ttmm) REVERT: C 69 ASN cc_start: 0.9142 (m-40) cc_final: 0.8732 (m110) REVERT: C 260 ILE cc_start: 0.8492 (mm) cc_final: 0.8270 (tp) REVERT: F 552 ASP cc_start: 0.8507 (m-30) cc_final: 0.7963 (m-30) REVERT: L 18 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8422 (ttp80) REVERT: I 83 ARG cc_start: 0.8822 (mtm-85) cc_final: 0.8505 (mtm180) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3100 time to fit residues: 43.6762 Evaluate side-chains 76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN F 551 GLN F 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.033350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.026428 restraints weight = 100294.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.027416 restraints weight = 54748.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.028123 restraints weight = 36891.299| |-----------------------------------------------------------------------------| r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13023 Z= 0.134 Angle : 0.573 7.816 17751 Z= 0.275 Chirality : 0.043 0.228 2034 Planarity : 0.004 0.052 2220 Dihedral : 6.831 59.776 2337 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.22), residues: 1557 helix: 0.73 (0.39), residues: 201 sheet: -1.70 (0.22), residues: 477 loop : -1.22 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 531 HIS 0.003 0.001 HIS I 100D PHE 0.011 0.001 PHE F 582 TYR 0.009 0.001 TYR J 91 ARG 0.004 0.000 ARG J 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00288 ( 12) link_NAG-ASN : angle 2.93910 ( 36) link_ALPHA1-6 : bond 0.00465 ( 3) link_ALPHA1-6 : angle 1.91025 ( 9) link_BETA1-4 : bond 0.00361 ( 9) link_BETA1-4 : angle 1.50380 ( 27) link_ALPHA1-2 : bond 0.00141 ( 3) link_ALPHA1-2 : angle 2.34274 ( 9) link_ALPHA1-3 : bond 0.01503 ( 3) link_ALPHA1-3 : angle 0.67952 ( 9) hydrogen bonds : bond 0.02815 ( 324) hydrogen bonds : angle 5.14862 ( 891) SS BOND : bond 0.00133 ( 6) SS BOND : angle 0.96306 ( 12) covalent geometry : bond 0.00292 (12987) covalent geometry : angle 0.55077 (17649) *********************** 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 : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 552 ASP cc_start: 0.8579 (m-30) cc_final: 0.8091 (m-30) REVERT: J 33 LEU cc_start: 0.9201 (tp) cc_final: 0.8869 (tp) REVERT: G 83 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8598 (mtm180) REVERT: B 69 ASN cc_start: 0.9087 (m-40) cc_final: 0.8742 (m110) REVERT: B 260 ILE cc_start: 0.8647 (mm) cc_final: 0.8399 (tp) REVERT: E 552 ASP cc_start: 0.8738 (m-30) cc_final: 0.8220 (m-30) REVERT: K 75 ILE cc_start: 0.9223 (mp) cc_final: 0.8995 (pt) REVERT: H 75 LYS cc_start: 0.9587 (ttmm) cc_final: 0.9312 (ttmm) REVERT: C 69 ASN cc_start: 0.9161 (m-40) cc_final: 0.8764 (m110) REVERT: C 260 ILE cc_start: 0.8530 (mm) cc_final: 0.8314 (tp) REVERT: F 552 ASP cc_start: 0.8580 (m-30) cc_final: 0.8109 (m-30) REVERT: I 83 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8528 (mtm180) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2923 time to fit residues: 41.3750 Evaluate side-chains 73 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.033802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.026860 restraints weight = 98648.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.027867 restraints weight = 53503.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.028571 restraints weight = 35793.885| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13023 Z= 0.108 Angle : 0.552 8.378 17751 Z= 0.265 Chirality : 0.042 0.218 2034 Planarity : 0.004 0.051 2220 Dihedral : 6.364 58.015 2337 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.22), residues: 1557 helix: 0.76 (0.39), residues: 201 sheet: -1.48 (0.23), residues: 450 loop : -1.21 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.003 0.001 HIS H 96 PHE 0.008 0.001 PHE A 234 TYR 0.008 0.001 TYR I 91 ARG 0.010 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 12) link_NAG-ASN : angle 2.84617 ( 36) link_ALPHA1-6 : bond 0.00616 ( 3) link_ALPHA1-6 : angle 1.68263 ( 9) link_BETA1-4 : bond 0.00346 ( 9) link_BETA1-4 : angle 1.44355 ( 27) link_ALPHA1-2 : bond 0.00229 ( 3) link_ALPHA1-2 : angle 2.46476 ( 9) link_ALPHA1-3 : bond 0.01582 ( 3) link_ALPHA1-3 : angle 0.61341 ( 9) hydrogen bonds : bond 0.02733 ( 324) hydrogen bonds : angle 4.99419 ( 891) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.90272 ( 12) covalent geometry : bond 0.00238 (12987) covalent geometry : angle 0.53046 (17649) *********************** 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 104 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.347 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: D 552 ASP cc_start: 0.8613 (m-30) cc_final: 0.8159 (m-30) REVERT: J 33 LEU cc_start: 0.9211 (tp) cc_final: 0.8835 (tp) REVERT: G 83 ARG cc_start: 0.8893 (mtm-85) cc_final: 0.8585 (mtm180) REVERT: B 69 ASN cc_start: 0.9083 (m-40) cc_final: 0.8763 (m110) REVERT: B 260 ILE cc_start: 0.8648 (mm) cc_final: 0.8421 (tp) REVERT: E 552 ASP cc_start: 0.8728 (m-30) cc_final: 0.8225 (m-30) REVERT: K 75 ILE cc_start: 0.9224 (mp) cc_final: 0.8965 (pt) REVERT: H 75 LYS cc_start: 0.9564 (ttmm) cc_final: 0.9290 (ttmm) REVERT: C 69 ASN cc_start: 0.9161 (m-40) cc_final: 0.8783 (m110) REVERT: C 260 ILE cc_start: 0.8622 (mm) cc_final: 0.8386 (tp) REVERT: F 552 ASP cc_start: 0.8629 (m-30) cc_final: 0.8140 (m-30) REVERT: F 556 CYS cc_start: 0.9173 (m) cc_final: 0.8936 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2814 time to fit residues: 41.3907 Evaluate side-chains 73 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 104 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 126 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 516 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.033785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.026989 restraints weight = 98353.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.028003 restraints weight = 52954.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.028721 restraints weight = 35174.489| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13023 Z= 0.108 Angle : 0.545 8.464 17751 Z= 0.262 Chirality : 0.042 0.205 2034 Planarity : 0.004 0.050 2220 Dihedral : 6.005 52.038 2337 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1557 helix: 0.77 (0.39), residues: 201 sheet: -1.37 (0.23), residues: 480 loop : -1.10 (0.23), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS I 96 PHE 0.010 0.001 PHE L 71 TYR 0.007 0.001 TYR J 91 ARG 0.008 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 2.82078 ( 36) link_ALPHA1-6 : bond 0.00643 ( 3) link_ALPHA1-6 : angle 1.54551 ( 9) link_BETA1-4 : bond 0.00347 ( 9) link_BETA1-4 : angle 1.48793 ( 27) link_ALPHA1-2 : bond 0.00258 ( 3) link_ALPHA1-2 : angle 2.45554 ( 9) link_ALPHA1-3 : bond 0.01487 ( 3) link_ALPHA1-3 : angle 0.66421 ( 9) hydrogen bonds : bond 0.02730 ( 324) hydrogen bonds : angle 4.89466 ( 891) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.80369 ( 12) covalent geometry : bond 0.00238 (12987) covalent geometry : angle 0.52407 (17649) ********************** 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 105 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.453 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: D 552 ASP cc_start: 0.8677 (m-30) cc_final: 0.8287 (m-30) REVERT: J 33 LEU cc_start: 0.9205 (tp) cc_final: 0.8804 (tp) REVERT: G 83 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8607 (mtm180) REVERT: B 69 ASN cc_start: 0.9107 (m-40) cc_final: 0.8778 (m110) REVERT: B 260 ILE cc_start: 0.8637 (mm) cc_final: 0.8420 (tp) REVERT: E 552 ASP cc_start: 0.8715 (m-30) cc_final: 0.8227 (m-30) REVERT: K 75 ILE cc_start: 0.9299 (mp) cc_final: 0.9048 (pt) REVERT: H 75 LYS cc_start: 0.9533 (ttmm) cc_final: 0.9271 (ttmm) REVERT: C 69 ASN cc_start: 0.9150 (m-40) cc_final: 0.8736 (m110) REVERT: C 260 ILE cc_start: 0.8596 (mm) cc_final: 0.8395 (tp) REVERT: F 552 ASP cc_start: 0.8581 (m-30) cc_final: 0.8008 (m-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2974 time to fit residues: 44.1588 Evaluate side-chains 73 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 92 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.033082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026266 restraints weight = 100800.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027258 restraints weight = 54639.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.027951 restraints weight = 36522.258| |-----------------------------------------------------------------------------| r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13023 Z= 0.172 Angle : 0.586 7.947 17751 Z= 0.281 Chirality : 0.042 0.221 2034 Planarity : 0.004 0.051 2220 Dihedral : 6.017 48.632 2337 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1557 helix: 0.63 (0.38), residues: 204 sheet: -1.47 (0.21), residues: 564 loop : -0.88 (0.24), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 104 HIS 0.016 0.001 HIS D 516 PHE 0.023 0.001 PHE D 582 TYR 0.011 0.001 TYR H 90 ARG 0.008 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 12) link_NAG-ASN : angle 2.82767 ( 36) link_ALPHA1-6 : bond 0.00525 ( 3) link_ALPHA1-6 : angle 1.63762 ( 9) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.61463 ( 27) link_ALPHA1-2 : bond 0.00143 ( 3) link_ALPHA1-2 : angle 2.30893 ( 9) link_ALPHA1-3 : bond 0.01222 ( 3) link_ALPHA1-3 : angle 0.81358 ( 9) hydrogen bonds : bond 0.02832 ( 324) hydrogen bonds : angle 4.98692 ( 891) SS BOND : bond 0.00160 ( 6) SS BOND : angle 0.88930 ( 12) covalent geometry : bond 0.00374 (12987) covalent geometry : angle 0.56556 (17649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3448.25 seconds wall clock time: 61 minutes 12.07 seconds (3672.07 seconds total)