Starting phenix.real_space_refine on Sat Aug 23 09:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.map" model { file = "/net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nch_12266/08_2025/7nch_12266.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 C 3408 2.51 5 N 972 2.21 5 O 1116 1.98 5 H 5796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11292 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "D" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "E" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "F" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "J" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "K" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Chain: "L" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 941 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain breaks: 1 Time building chain proxies: 2.52, per 1000 atoms: 0.22 Number of scatterers: 11292 At special positions: 0 Unit cell: (100.1, 89.1, 53.9, 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) O 1116 8.00 N 972 7.00 C 3408 6.00 H 5796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 279.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21 removed outlier: 3.537A pdb=" N ALA B 17 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 18 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 19 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 20 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 21 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 17 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 19 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 21 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA D 17 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA D 19 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 21 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E 19 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA F 19 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS F 21 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 removed outlier: 3.516A pdb=" N GLY A 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 41 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR D 39 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 8.236A pdb=" N GLY A 51 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA B 53 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA A 53 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 55 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 55 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.752A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N HIS C 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA D 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N VAL C 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N VAL D 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR C 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL D 49 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N GLY E 51 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N GLY D 51 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA E 53 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA D 53 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL E 55 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL D 55 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.929A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL E 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 72 removed outlier: 5.999A pdb=" N ALA A 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR B 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR C 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL B 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 85 through 88 removed outlier: 6.592A pdb=" N GLY A 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 86 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 86 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 16 through 21 removed outlier: 3.518A pdb=" N ALA H 17 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA H 19 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU G 20 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS H 21 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA I 17 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA I 19 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS I 21 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 17 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA J 19 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS J 21 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA K 19 " --> pdb=" O ALA J 18 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS K 21 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 19 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS L 21 " --> pdb=" O GLU K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 39 through 41 removed outlier: 3.511A pdb=" N GLY G 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY I 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 49 through 55 removed outlier: 4.687A pdb=" N VAL G 49 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N GLY H 51 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY G 51 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ALA H 53 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ALA G 53 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL H 55 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL G 55 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N HIS H 50 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA I 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N VAL H 52 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 10.793A pdb=" N VAL I 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N THR H 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N HIS I 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA J 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N VAL I 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL J 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR I 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 9.085A pdb=" N HIS J 50 " --> pdb=" O GLY K 51 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA K 53 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N VAL J 52 " --> pdb=" O ALA K 53 " (cutoff:3.500A) removed outlier: 10.885A pdb=" N VAL K 55 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR J 54 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N HIS K 50 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA L 53 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N VAL K 52 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N VAL L 55 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N THR K 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 66 removed outlier: 7.089A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL J 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL K 63 " --> pdb=" O THR L 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 85 through 88 removed outlier: 6.536A pdb=" N GLY G 86 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER I 87 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE H 88 " --> pdb=" O SER I 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 86 " --> pdb=" O ALA J 85 " (cutoff:3.500A) 50 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 0.97: 4723 0.97 - 1.13: 1073 1.13 - 1.28: 984 1.28 - 1.44: 1089 1.44 - 1.59: 3423 Bond restraints: 11292 Sorted by residual: bond pdb=" C GLY F 86 " pdb=" N SER F 87 " ideal model delta sigma weight residual 1.330 1.359 -0.029 1.26e-02 6.30e+03 5.24e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.44e-02 4.82e+03 5.21e+00 bond pdb=" C ALA L 18 " pdb=" N ALA L 19 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.26e-02 6.30e+03 5.05e+00 bond pdb=" C GLU L 20 " pdb=" N LYS L 21 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.45e-02 4.76e+03 4.94e+00 bond pdb=" C ALA F 18 " pdb=" N ALA F 19 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.26e-02 6.30e+03 4.83e+00 ... (remaining 11287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.21: 20525 7.21 - 14.41: 1 14.41 - 21.62: 0 21.62 - 28.82: 0 28.82 - 36.03: 6 Bond angle restraints: 20532 Sorted by residual: angle pdb=" N THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 110.00 73.97 36.03 3.00e+00 1.11e-01 1.44e+02 angle pdb=" N THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 110.00 74.30 35.70 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C THR I 44 " pdb=" CA THR I 44 " pdb=" HA THR I 44 " ideal model delta sigma weight residual 109.00 74.27 34.73 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 109.00 74.54 34.46 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB THR C 44 " pdb=" CA THR C 44 " pdb=" HA THR C 44 " ideal model delta sigma weight residual 109.00 79.67 29.33 3.00e+00 1.11e-01 9.56e+01 ... (remaining 20527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4426 17.96 - 35.93: 292 35.93 - 53.89: 140 53.89 - 71.85: 278 71.85 - 89.81: 24 Dihedral angle restraints: 5160 sinusoidal: 2904 harmonic: 2256 Sorted by residual: dihedral pdb=" CA ILE A 88 " pdb=" C ILE A 88 " pdb=" N ALA A 89 " pdb=" CA ALA A 89 " ideal model delta harmonic sigma weight residual 180.00 151.02 28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ILE G 88 " pdb=" C ILE G 88 " pdb=" N ALA G 89 " pdb=" CA ALA G 89 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA VAL A 74 " pdb=" C VAL A 74 " pdb=" N THR A 75 " pdb=" CA THR A 75 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 681 0.092 - 0.185: 244 0.185 - 0.277: 55 0.277 - 0.369: 2 0.369 - 0.461: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA THR C 44 " pdb=" N THR C 44 " pdb=" C THR C 44 " pdb=" CB THR C 44 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA THR I 44 " pdb=" N THR I 44 " pdb=" C THR I 44 " pdb=" CB THR I 44 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA ILE G 88 " pdb=" N ILE G 88 " pdb=" C ILE G 88 " pdb=" CB ILE G 88 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 981 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 24 " -0.030 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" CD GLN L 24 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN L 24 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN L 24 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN L 24 " -0.001 2.00e-02 2.50e+03 pdb="HE22 GLN L 24 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 39 " -0.022 2.00e-02 2.50e+03 2.51e-02 1.88e+01 pdb=" CG TYR H 39 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR H 39 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 39 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR H 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR H 39 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 39 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR H 39 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 TYR H 39 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR H 39 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR H 39 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR H 39 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 24 " -0.029 2.00e-02 2.50e+03 3.49e-02 1.82e+01 pdb=" CD GLN F 24 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLN F 24 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN F 24 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN F 24 " -0.000 2.00e-02 2.50e+03 pdb="HE22 GLN F 24 " -0.051 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.23: 603 2.23 - 2.80: 22255 2.80 - 3.36: 25990 3.36 - 3.93: 32857 3.93 - 4.50: 50921 Nonbonded interactions: 132626 Sorted by model distance: nonbonded pdb=" HG SER E 87 " pdb=" O SER F 87 " model vdw 1.662 2.450 nonbonded pdb=" H THR I 44 " pdb=" HA THR I 44 " model vdw 1.664 1.816 nonbonded pdb=" HG SER K 87 " pdb=" O SER L 87 " model vdw 1.667 2.450 nonbonded pdb=" H THR C 44 " pdb=" HA THR C 44 " model vdw 1.674 1.816 nonbonded pdb=" HG1 THR C 44 " pdb=" O THR D 44 " model vdw 1.726 2.450 ... (remaining 132621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4929 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 : 0.013 0.069 5496 Z= 0.729 Angle : 1.606 7.507 7416 Z= 0.967 Chirality : 0.095 0.461 984 Planarity : 0.005 0.026 924 Dihedral : 14.676 89.811 1848 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.19 % Allowed : 2.78 % Favored : 97.04 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.15), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.12), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.059 0.014 TYR H 39 HIS 0.015 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.01308 ( 5496) covalent geometry : angle 1.60592 ( 7416) hydrogen bonds : bond 0.39029 ( 50) hydrogen bonds : angle 12.16636 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.290 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 outliers start: 1 outliers final: 1 residues processed: 155 average time/residue: 0.2159 time to fit residues: 41.7353 Evaluate side-chains 85 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN H 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.210779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.175940 restraints weight = 23913.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.187915 restraints weight = 10811.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.195107 restraints weight = 5635.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.199827 restraints weight = 3286.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.202891 restraints weight = 2055.816| |-----------------------------------------------------------------------------| r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5262 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5496 Z= 0.194 Angle : 0.738 6.603 7416 Z= 0.435 Chirality : 0.053 0.372 984 Planarity : 0.002 0.012 924 Dihedral : 8.256 26.484 805 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.22 % Allowed : 13.70 % Favored : 84.07 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.17), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYR A 39 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5496) covalent geometry : angle 0.73810 ( 7416) hydrogen bonds : bond 0.13464 ( 50) hydrogen bonds : angle 10.15034 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.293 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 outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1913 time to fit residues: 23.9594 Evaluate side-chains 81 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.204014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.170089 restraints weight = 23924.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.181883 restraints weight = 10601.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.189158 restraints weight = 5454.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.193793 restraints weight = 3154.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.196735 restraints weight = 1954.375| |-----------------------------------------------------------------------------| r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5419 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5496 Z= 0.237 Angle : 0.758 6.600 7416 Z= 0.444 Chirality : 0.053 0.376 984 Planarity : 0.004 0.017 924 Dihedral : 7.943 26.334 805 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 5.00 % Allowed : 16.30 % Favored : 78.70 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.45 (0.18), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR A 39 HIS 0.002 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 5496) covalent geometry : angle 0.75824 ( 7416) hydrogen bonds : bond 0.10058 ( 50) hydrogen bonds : angle 9.28835 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 22 residues processed: 85 average time/residue: 0.1705 time to fit residues: 19.2534 Evaluate side-chains 86 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 46 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 35 optimal weight: 0.0070 chunk 68 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4896 r_free = 0.4896 target = 0.204935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.172831 restraints weight = 23723.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.183483 restraints weight = 10592.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.190353 restraints weight = 5383.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.194645 restraints weight = 3090.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.197604 restraints weight = 1919.983| |-----------------------------------------------------------------------------| r_work (final): 0.4872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5349 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5496 Z= 0.120 Angle : 0.577 5.473 7416 Z= 0.335 Chirality : 0.053 0.378 984 Planarity : 0.002 0.013 924 Dihedral : 6.611 22.834 805 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.78 % Allowed : 17.59 % Favored : 79.63 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.14), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR A 39 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5496) covalent geometry : angle 0.57653 ( 7416) hydrogen bonds : bond 0.08282 ( 50) hydrogen bonds : angle 8.61510 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 46 GLU cc_start: 0.8667 (pp20) cc_final: 0.8454 (pp20) outliers start: 15 outliers final: 11 residues processed: 77 average time/residue: 0.1493 time to fit residues: 15.8284 Evaluate side-chains 74 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.4884 r_free = 0.4884 target = 0.202171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.168307 restraints weight = 24312.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.180451 restraints weight = 10455.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.187808 restraints weight = 5351.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.192242 restraints weight = 3054.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.195057 restraints weight = 1869.484| |-----------------------------------------------------------------------------| r_work (final): 0.4860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5496 Z= 0.122 Angle : 0.541 5.320 7416 Z= 0.315 Chirality : 0.052 0.370 984 Planarity : 0.002 0.011 924 Dihedral : 6.029 20.106 805 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.41 % Allowed : 17.59 % Favored : 80.00 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR A 39 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5496) covalent geometry : angle 0.54098 ( 7416) hydrogen bonds : bond 0.06858 ( 50) hydrogen bonds : angle 8.03373 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.1513 time to fit residues: 15.6292 Evaluate side-chains 78 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.198754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.166063 restraints weight = 24933.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.178194 restraints weight = 10698.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.185391 restraints weight = 5457.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.189791 restraints weight = 3107.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.192606 restraints weight = 1903.532| |-----------------------------------------------------------------------------| r_work (final): 0.4822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5445 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5496 Z= 0.160 Angle : 0.579 4.538 7416 Z= 0.335 Chirality : 0.052 0.383 984 Planarity : 0.002 0.011 924 Dihedral : 6.352 19.606 805 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 3.89 % Allowed : 18.33 % Favored : 77.78 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.37 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR A 39 HIS 0.004 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5496) covalent geometry : angle 0.57942 ( 7416) hydrogen bonds : bond 0.06369 ( 50) hydrogen bonds : angle 7.66116 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.1561 time to fit residues: 18.0590 Evaluate side-chains 83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 overall best weight: 0.2554 ------------------------------------------------------------------------------- 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 = 0.4910 r_free = 0.4910 target = 0.203816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.168883 restraints weight = 23801.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.180986 restraints weight = 10395.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.188319 restraints weight = 5380.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.192820 restraints weight = 3086.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.195781 restraints weight = 1914.546| |-----------------------------------------------------------------------------| r_work (final): 0.4857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5380 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5496 Z= 0.104 Angle : 0.520 4.723 7416 Z= 0.297 Chirality : 0.053 0.363 984 Planarity : 0.002 0.019 924 Dihedral : 5.414 17.564 805 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.93 % Allowed : 20.74 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR I 39 HIS 0.001 0.000 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 5496) covalent geometry : angle 0.52009 ( 7416) hydrogen bonds : bond 0.06250 ( 50) hydrogen bonds : angle 7.42555 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 70 average time/residue: 0.1642 time to fit residues: 15.6028 Evaluate side-chains 68 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.4893 r_free = 0.4893 target = 0.201765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.167251 restraints weight = 24431.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.179429 restraints weight = 10636.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.186729 restraints weight = 5498.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.191265 restraints weight = 3162.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.194088 restraints weight = 1968.127| |-----------------------------------------------------------------------------| r_work (final): 0.4859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5458 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5496 Z= 0.109 Angle : 0.512 5.370 7416 Z= 0.294 Chirality : 0.052 0.377 984 Planarity : 0.002 0.011 924 Dihedral : 5.334 17.141 805 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 1.67 % Allowed : 21.48 % Favored : 76.85 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.93 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.16), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 39 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5496) covalent geometry : angle 0.51174 ( 7416) hydrogen bonds : bond 0.05917 ( 50) hydrogen bonds : angle 7.28493 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 61 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5951 (mt-10) REVERT: H 79 GLN cc_start: 0.7731 (tp40) cc_final: 0.7529 (tp40) outliers start: 9 outliers final: 9 residues processed: 67 average time/residue: 0.1337 time to fit residues: 12.8735 Evaluate side-chains 73 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 41 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4872 r_free = 0.4872 target = 0.197411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.165316 restraints weight = 23869.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.176505 restraints weight = 10492.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.183406 restraints weight = 5477.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.187724 restraints weight = 3157.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.190303 restraints weight = 1921.592| |-----------------------------------------------------------------------------| r_work (final): 0.4833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5499 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5496 Z= 0.128 Angle : 0.518 5.216 7416 Z= 0.298 Chirality : 0.052 0.378 984 Planarity : 0.002 0.009 924 Dihedral : 5.410 17.407 805 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 1.67 % Allowed : 22.04 % Favored : 76.30 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.04 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR I 39 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5496) covalent geometry : angle 0.51775 ( 7416) hydrogen bonds : bond 0.05764 ( 50) hydrogen bonds : angle 7.11800 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 LYS cc_start: 0.5422 (mttt) cc_final: 0.5062 (tptt) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.1428 time to fit residues: 13.6487 Evaluate side-chains 73 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4843 r_free = 0.4843 target = 0.195705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.163193 restraints weight = 25020.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.175020 restraints weight = 10964.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.181926 restraints weight = 5737.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.186293 restraints weight = 3318.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.188929 restraints weight = 2018.394| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5504 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 5496 Z= 0.145 Angle : 0.537 5.341 7416 Z= 0.309 Chirality : 0.053 0.378 984 Planarity : 0.002 0.010 924 Dihedral : 5.748 17.857 805 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 1.67 % Allowed : 22.78 % Favored : 75.56 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR I 39 HIS 0.002 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 5496) covalent geometry : angle 0.53666 ( 7416) hydrogen bonds : bond 0.05799 ( 50) hydrogen bonds : angle 6.96725 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 LYS cc_start: 0.5102 (mttt) cc_final: 0.4747 (tptt) REVERT: I 21 LYS cc_start: 0.8172 (tttt) cc_final: 0.7791 (tptm) REVERT: K 21 LYS cc_start: 0.7677 (tttt) cc_final: 0.7349 (tptt) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.1299 time to fit residues: 12.0902 Evaluate side-chains 72 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4813 r_free = 0.4813 target = 0.192159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.162491 restraints weight = 24900.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.171566 restraints weight = 11467.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.178754 restraints weight = 6052.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.183054 restraints weight = 3479.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.185744 restraints weight = 2124.350| |-----------------------------------------------------------------------------| r_work (final): 0.4776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.7588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5496 Z= 0.169 Angle : 0.574 5.508 7416 Z= 0.331 Chirality : 0.053 0.379 984 Planarity : 0.002 0.015 924 Dihedral : 6.071 19.987 805 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.97 % Favored : 85.03 % Rotamer: Outliers : 2.22 % Allowed : 22.59 % Favored : 75.19 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR I 39 HIS 0.002 0.000 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5496) covalent geometry : angle 0.57386 ( 7416) hydrogen bonds : bond 0.05909 ( 50) hydrogen bonds : angle 6.91363 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.22 seconds wall clock time: 45 minutes 34.53 seconds (2734.53 seconds total)