Starting phenix.real_space_refine on Sat Dec 9 13:57:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_12266.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_12266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_12266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_12266.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nch_12266/12_2023/7nch_12266.pdb" } resolution = 3.84 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= 0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/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: 5.14, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 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: 8.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 3.52 Time building geometry restraints manager: 8.90 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: 73.97 - 85.28: 6 85.28 - 96.58: 0 96.58 - 107.88: 2613 107.88 - 119.19: 14178 119.19 - 130.49: 3735 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: 4303 17.96 - 35.93: 240 35.93 - 53.89: 47 53.89 - 71.85: 222 71.85 - 89.81: 24 Dihedral angle restraints: 4836 sinusoidal: 2580 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 4833 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 1.850 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 1.850 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 1.850 ... (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 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.180 Extract box with map and model: 3.880 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 36.580 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.230 ------------------------------------------------------------------------------- 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= 0.900 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 (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: -3.70 (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 HIS 0.015 0.005 HIS H 50 TYR 0.059 0.014 TYR H 39 *********************** 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 fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.826 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: 0.4306 time to fit residues: 83.5604 Evaluate side-chains 85 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1213 time to fit residues: 1.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5117 moved from start: 0.3749 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= 0.237 Angle : 0.727 6.908 7416 Z= 0.428 Chirality : 0.053 0.387 984 Planarity : 0.002 0.016 924 Dihedral : 8.282 26.611 804 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.22 % Allowed : 14.07 % Favored : 83.70 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.90 (0.17), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.13), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 TYR 0.021 0.003 TYR A 39 *********************** 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 98 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.826 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 outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.3793 time to fit residues: 46.7646 Evaluate side-chains 78 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1210 time to fit residues: 2.7908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 moved from start: 0.4769 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= 0.301 Angle : 0.732 6.414 7416 Z= 0.428 Chirality : 0.053 0.396 984 Planarity : 0.003 0.017 924 Dihedral : 7.764 26.273 804 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.96 % Allowed : 16.67 % Favored : 80.37 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.40 (0.18), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.14), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.015 0.003 TYR A 39 *********************** 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 85 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 13 residues processed: 79 average time/residue: 0.3820 time to fit residues: 39.4580 Evaluate side-chains 77 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1197 time to fit residues: 3.8807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.0000 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5291 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5496 Z= 0.182 Angle : 0.590 5.510 7416 Z= 0.344 Chirality : 0.052 0.381 984 Planarity : 0.002 0.011 924 Dihedral : 6.780 22.880 804 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 1.30 % Allowed : 15.74 % Favored : 82.96 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.28 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.14), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS H 50 TYR 0.010 0.002 TYR A 39 *********************** 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 73 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 68 average time/residue: 0.3574 time to fit residues: 32.8965 Evaluate side-chains 64 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.808 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1290 time to fit residues: 1.7932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5496 Z= 0.208 Angle : 0.590 5.675 7416 Z= 0.342 Chirality : 0.053 0.388 984 Planarity : 0.002 0.011 924 Dihedral : 6.455 21.173 804 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.93 % Allowed : 19.07 % Favored : 80.00 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.31 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 TYR 0.009 0.002 TYR A 39 *********************** 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 68 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.3126 time to fit residues: 28.6163 Evaluate side-chains 63 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1233 time to fit residues: 1.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 13 optimal weight: 0.0060 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 0.0570 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5269 moved from start: 0.6151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5496 Z= 0.152 Angle : 0.534 5.617 7416 Z= 0.306 Chirality : 0.053 0.375 984 Planarity : 0.002 0.017 924 Dihedral : 5.671 17.970 804 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.74 % Allowed : 19.44 % Favored : 79.81 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.01 (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 HIS 0.001 0.000 HIS L 50 TYR 0.006 0.001 TYR A 39 *********************** 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 70 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 68 average time/residue: 0.3058 time to fit residues: 29.2115 Evaluate side-chains 61 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1231 time to fit residues: 1.2613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.0000 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.6459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5496 Z= 0.178 Angle : 0.527 4.699 7416 Z= 0.306 Chirality : 0.052 0.391 984 Planarity : 0.002 0.011 924 Dihedral : 5.637 17.793 804 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 0.37 % Allowed : 21.11 % Favored : 78.52 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.08 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 50 TYR 0.007 0.001 TYR A 39 *********************** 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 64 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.3019 time to fit residues: 26.6877 Evaluate side-chains 61 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.874 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1221 time to fit residues: 1.4657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5367 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5496 Z= 0.176 Angle : 0.527 4.409 7416 Z= 0.304 Chirality : 0.052 0.391 984 Planarity : 0.002 0.011 924 Dihedral : 5.634 17.590 804 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 1.48 % Allowed : 21.30 % Favored : 77.22 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.13 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 TYR 0.006 0.001 TYR I 39 *********************** 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 64 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.2795 time to fit residues: 24.1486 Evaluate side-chains 61 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1202 time to fit residues: 2.0351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.7211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5496 Z= 0.302 Angle : 0.649 5.087 7416 Z= 0.378 Chirality : 0.054 0.397 984 Planarity : 0.003 0.014 924 Dihedral : 6.685 22.439 804 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 0.37 % Allowed : 22.22 % Favored : 77.41 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.58 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 50 TYR 0.007 0.002 TYR I 39 *********************** 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 63 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.3299 time to fit residues: 28.6820 Evaluate side-chains 58 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 moved from start: 0.7394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5496 Z= 0.206 Angle : 0.570 4.708 7416 Z= 0.329 Chirality : 0.053 0.390 984 Planarity : 0.002 0.017 924 Dihedral : 6.218 19.481 804 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.56 % Allowed : 23.33 % Favored : 76.11 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.55 (0.19), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 TYR 0.007 0.001 TYR I 39 ********************** 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 62 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.2767 time to fit residues: 23.8064 Evaluate side-chains 60 residues out of total 540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1183 time to fit residues: 1.1770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.193092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.162339 restraints weight = 25166.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.173624 restraints weight = 11231.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.180771 restraints weight = 5773.627| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5496 Z= 0.202 Angle : 0.555 4.915 7416 Z= 0.322 Chirality : 0.053 0.391 984 Planarity : 0.002 0.013 924 Dihedral : 5.879 17.732 804 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer: Outliers : 0.19 % Allowed : 23.33 % Favored : 76.48 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % 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: -4.48 (0.20), residues: 768 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.15), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 TYR 0.007 0.001 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3195.93 seconds wall clock time: 57 minutes 10.00 seconds (3430.00 seconds total)