Starting phenix.real_space_refine on Sat Mar 16 04:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nrv_0497/03_2024/6nrv_0497.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.033 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 8554 2.51 5 N 2236 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13637 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "B" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "E" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "F" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "G" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "H" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "I" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "J" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "K" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "L" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "M" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1049 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 7.32, per 1000 atoms: 0.54 Number of scatterers: 13637 At special positions: 0 Unit cell: (87.2, 88.29, 151.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 2808 8.00 N 2236 7.00 C 8554 6.00 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: 5.11 Conformation dependent library (CDL) restraints added in 2.5 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 39 sheets defined 3.4% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 98 through 102 removed outlier: 4.004A pdb=" N GLY A 102 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 removed outlier: 4.004A pdb=" N GLY B 102 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY C 102 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY D 102 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY E 102 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY F 102 " --> pdb=" O ALA F 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY G 102 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY H 102 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 102 removed outlier: 4.006A pdb=" N GLY I 102 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY J 102 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY K 102 " --> pdb=" O ALA K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY L 102 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 4.005A pdb=" N GLY M 102 " --> pdb=" O ALA M 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 removed outlier: 7.774A pdb=" N LEU B 31 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 8 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 141 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP B 70 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL B 76 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.942A pdb=" N SER C 10 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 141 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 70 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 76 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 10 removed outlier: 4.535A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 70 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL D 76 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 47 Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 47 Processing sheet with id=AA9, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB1, first strand: chain 'C' and resid 73 through 79 removed outlier: 6.342A pdb=" N VAL C 76 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP C 70 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN C 67 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 138 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 31 removed outlier: 7.939A pdb=" N LEU F 31 " --> pdb=" O THR D 6 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 70 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL F 76 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 43 through 47 Processing sheet with id=AB4, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.071A pdb=" N SER G 10 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP E 70 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL E 76 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 43 through 47 Processing sheet with id=AB7, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=AB8, first strand: chain 'H' and resid 30 through 31 removed outlier: 8.033A pdb=" N LEU H 31 " --> pdb=" O THR F 6 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR F 8 " --> pdb=" O LEU H 31 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU H 141 " --> pdb=" O LYS F 3 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL H 138 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN H 67 " --> pdb=" O VAL H 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP H 70 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL H 76 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 43 through 47 Processing sheet with id=AC1, first strand: chain 'F' and resid 94 through 96 Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.915A pdb=" N SER I 10 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP G 70 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 76 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 43 through 47 Processing sheet with id=AC4, first strand: chain 'G' and resid 94 through 96 Processing sheet with id=AC5, first strand: chain 'H' and resid 3 through 10 removed outlier: 3.538A pdb=" N LEU J 141 " --> pdb=" O LYS H 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL J 138 " --> pdb=" O GLN J 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN J 67 " --> pdb=" O VAL J 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP J 70 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL J 76 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 43 through 47 Processing sheet with id=AC7, first strand: chain 'H' and resid 94 through 96 Processing sheet with id=AC8, first strand: chain 'I' and resid 43 through 47 Processing sheet with id=AC9, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'I' and resid 73 through 79 removed outlier: 6.341A pdb=" N VAL I 76 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP I 70 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN I 67 " --> pdb=" O VAL I 138 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL I 138 " --> pdb=" O GLN I 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 3 through 10 removed outlier: 4.535A pdb=" N VAL L 138 " --> pdb=" O GLN L 67 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLN L 67 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP L 70 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL L 76 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 43 through 47 Processing sheet with id=AD4, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AD5, first strand: chain 'K' and resid 30 through 31 removed outlier: 4.073A pdb=" N SER M 10 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU K 141 " --> pdb=" O LYS M 3 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL K 138 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN K 67 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP K 70 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL K 76 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 43 through 47 Processing sheet with id=AD7, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AD8, first strand: chain 'L' and resid 43 through 47 Processing sheet with id=AD9, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AE1, first strand: chain 'M' and resid 43 through 47 Processing sheet with id=AE2, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AE3, first strand: chain 'M' and resid 73 through 79 removed outlier: 6.341A pdb=" N VAL M 76 " --> pdb=" O ASP M 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP M 70 " --> pdb=" O VAL M 76 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 873 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: 3.67 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4425 1.34 - 1.46: 2530 1.46 - 1.57: 6799 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 13832 Sorted by residual: bond pdb=" CA VAL A 29 " pdb=" CB VAL A 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.26e+00 bond pdb=" CA VAL M 29 " pdb=" CB VAL M 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.20e+00 bond pdb=" CA VAL E 29 " pdb=" CB VAL E 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.20e+00 bond pdb=" CA VAL I 29 " pdb=" CB VAL I 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.19e+00 bond pdb=" CA VAL J 29 " pdb=" CB VAL J 29 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.09e+00 ... (remaining 13827 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.43: 413 106.43 - 113.29: 8187 113.29 - 120.14: 4125 120.14 - 127.00: 6049 127.00 - 133.86: 141 Bond angle restraints: 18915 Sorted by residual: angle pdb=" C ALA I 105 " pdb=" N SER I 106 " pdb=" CA SER I 106 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.68e+00 angle pdb=" C ALA D 105 " pdb=" N SER D 106 " pdb=" CA SER D 106 " ideal model delta sigma weight residual 121.54 126.83 -5.29 1.91e+00 2.74e-01 7.66e+00 angle pdb=" C ALA B 105 " pdb=" N SER B 106 " pdb=" CA SER B 106 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.64e+00 angle pdb=" C ALA J 105 " pdb=" N SER J 106 " pdb=" CA SER J 106 " ideal model delta sigma weight residual 121.54 126.81 -5.27 1.91e+00 2.74e-01 7.61e+00 angle pdb=" C ALA H 14 " pdb=" N ILE H 15 " pdb=" CA ILE H 15 " ideal model delta sigma weight residual 121.97 126.94 -4.97 1.80e+00 3.09e-01 7.61e+00 ... (remaining 18910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.39: 7384 8.39 - 16.78: 741 16.78 - 25.18: 182 25.18 - 33.57: 39 33.57 - 41.96: 39 Dihedral angle restraints: 8385 sinusoidal: 2912 harmonic: 5473 Sorted by residual: dihedral pdb=" CA ALA M 14 " pdb=" C ALA M 14 " pdb=" N ILE M 15 " pdb=" CA ILE M 15 " ideal model delta harmonic sigma weight residual 180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA K 14 " pdb=" C ALA K 14 " pdb=" N ILE K 15 " pdb=" CA ILE K 15 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ALA D 14 " pdb=" C ALA D 14 " pdb=" N ILE D 15 " pdb=" CA ILE D 15 " ideal model delta harmonic sigma weight residual 180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 8382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1312 0.030 - 0.061: 592 0.061 - 0.091: 230 0.091 - 0.121: 199 0.121 - 0.152: 85 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA VAL J 45 " pdb=" N VAL J 45 " pdb=" C VAL J 45 " pdb=" CB VAL J 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA VAL K 45 " pdb=" N VAL K 45 " pdb=" C VAL K 45 " pdb=" CB VAL K 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA VAL C 45 " pdb=" N VAL C 45 " pdb=" C VAL C 45 " pdb=" CB VAL C 45 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2415 not shown) Planarity restraints: 2392 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU I 95 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" CD GLU I 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU I 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU I 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 95 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" CD GLU K 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU K 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU K 95 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 95 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" CD GLU E 95 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU E 95 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU E 95 " 0.008 2.00e-02 2.50e+03 ... (remaining 2389 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 141 2.56 - 3.14: 12164 3.14 - 3.73: 19943 3.73 - 4.31: 29518 4.31 - 4.90: 47167 Nonbonded interactions: 108933 Sorted by model distance: nonbonded pdb=" OE2 GLU H 2 " pdb=" OG SER J 140 " model vdw 1.971 2.440 nonbonded pdb=" OE2 GLU J 2 " pdb=" OG SER L 140 " model vdw 1.973 2.440 nonbonded pdb=" NZ LYS D 3 " pdb=" O LEU F 17 " model vdw 2.043 2.520 nonbonded pdb=" O LEU G 17 " pdb=" NZ LYS I 3 " model vdw 2.063 2.520 nonbonded pdb=" O LEU A 17 " pdb=" NZ LYS C 3 " model vdw 2.079 2.520 ... (remaining 108928 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' selection = chain 'M' } 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 36.200 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.007 0.040 13832 Z= 0.480 Angle : 0.955 6.084 18915 Z= 0.506 Chirality : 0.051 0.152 2418 Planarity : 0.005 0.027 2392 Dihedral : 8.189 41.961 4849 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % 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: -4.59 (0.16), residues: 1872 helix: None (None), residues: 0 sheet: -3.10 (0.15), residues: 702 loop : -3.13 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP I 84 HIS 0.002 0.001 HIS L 50 PHE 0.008 0.002 PHE K 40 TYR 0.008 0.002 TYR K 33 ARG 0.006 0.003 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7021 (p0) cc_final: 0.6202 (m-30) REVERT: B 16 ASP cc_start: 0.7535 (p0) cc_final: 0.6656 (p0) REVERT: B 17 LEU cc_start: 0.8481 (tp) cc_final: 0.8113 (pt) REVERT: C 16 ASP cc_start: 0.7772 (p0) cc_final: 0.7392 (m-30) REVERT: C 21 ASP cc_start: 0.8811 (p0) cc_final: 0.8504 (p0) REVERT: D 16 ASP cc_start: 0.7881 (p0) cc_final: 0.7308 (p0) REVERT: D 21 ASP cc_start: 0.8597 (p0) cc_final: 0.8271 (p0) REVERT: E 16 ASP cc_start: 0.7314 (p0) cc_final: 0.6594 (m-30) REVERT: E 17 LEU cc_start: 0.8584 (tp) cc_final: 0.8319 (pt) REVERT: F 16 ASP cc_start: 0.7629 (p0) cc_final: 0.7413 (m-30) REVERT: F 19 GLN cc_start: 0.7982 (tp40) cc_final: 0.7689 (mm-40) REVERT: F 21 ASP cc_start: 0.8680 (p0) cc_final: 0.8315 (p0) REVERT: F 23 ASN cc_start: 0.8489 (m-40) cc_final: 0.8275 (m-40) REVERT: G 16 ASP cc_start: 0.7568 (p0) cc_final: 0.6964 (m-30) REVERT: G 17 LEU cc_start: 0.8671 (tp) cc_final: 0.8436 (pt) REVERT: G 21 ASP cc_start: 0.8784 (p0) cc_final: 0.8547 (p0) REVERT: I 17 LEU cc_start: 0.8747 (tp) cc_final: 0.8530 (pt) REVERT: I 21 ASP cc_start: 0.8451 (p0) cc_final: 0.7674 (p0) REVERT: J 16 ASP cc_start: 0.7204 (p0) cc_final: 0.6557 (p0) REVERT: J 17 LEU cc_start: 0.8305 (tp) cc_final: 0.8097 (pt) REVERT: K 17 LEU cc_start: 0.8391 (tp) cc_final: 0.8114 (pt) REVERT: K 25 LEU cc_start: 0.8700 (mt) cc_final: 0.8425 (mt) REVERT: L 16 ASP cc_start: 0.7135 (p0) cc_final: 0.6253 (m-30) REVERT: M 16 ASP cc_start: 0.7471 (p0) cc_final: 0.6812 (m-30) REVERT: M 21 ASP cc_start: 0.8471 (p0) cc_final: 0.8210 (p0) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.2628 time to fit residues: 145.7046 Evaluate side-chains 180 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 30.0000 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN H 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13832 Z= 0.234 Angle : 0.715 7.902 18915 Z= 0.381 Chirality : 0.047 0.157 2418 Planarity : 0.005 0.035 2392 Dihedral : 6.365 27.130 1950 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 1.97 % Allowed : 5.85 % Favored : 92.18 % Cbeta Deviations : 0.00 % 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: -3.19 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -1.83 (0.18), residues: 741 loop : -2.39 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 84 HIS 0.001 0.000 HIS L 50 PHE 0.014 0.002 PHE I 40 TYR 0.027 0.003 TYR B 43 ARG 0.001 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.7751 (p0) cc_final: 0.7175 (p0) REVERT: A 71 VAL cc_start: 0.8625 (m) cc_final: 0.8265 (m) REVERT: B 16 ASP cc_start: 0.7804 (p0) cc_final: 0.6894 (p0) REVERT: C 16 ASP cc_start: 0.7856 (p0) cc_final: 0.7054 (p0) REVERT: C 21 ASP cc_start: 0.8804 (p0) cc_final: 0.8434 (p0) REVERT: D 16 ASP cc_start: 0.7878 (p0) cc_final: 0.7411 (p0) REVERT: D 21 ASP cc_start: 0.9104 (p0) cc_final: 0.7958 (p0) REVERT: E 16 ASP cc_start: 0.7725 (p0) cc_final: 0.6884 (p0) REVERT: E 19 GLN cc_start: 0.7735 (tp40) cc_final: 0.7415 (tp40) REVERT: E 21 ASP cc_start: 0.8882 (p0) cc_final: 0.8426 (p0) REVERT: F 16 ASP cc_start: 0.7814 (p0) cc_final: 0.7122 (p0) REVERT: F 19 GLN cc_start: 0.7752 (tp40) cc_final: 0.7339 (mm-40) REVERT: F 21 ASP cc_start: 0.8603 (p0) cc_final: 0.8328 (p0) REVERT: G 16 ASP cc_start: 0.7915 (p0) cc_final: 0.7331 (p0) REVERT: G 19 GLN cc_start: 0.7888 (tp40) cc_final: 0.7673 (tp40) REVERT: G 21 ASP cc_start: 0.9018 (p0) cc_final: 0.8585 (p0) REVERT: G 23 ASN cc_start: 0.8835 (m-40) cc_final: 0.8381 (m-40) REVERT: I 21 ASP cc_start: 0.8796 (p0) cc_final: 0.7749 (p0) REVERT: J 16 ASP cc_start: 0.7471 (p0) cc_final: 0.7014 (p0) REVERT: K 16 ASP cc_start: 0.7439 (p0) cc_final: 0.7225 (p0) REVERT: K 19 GLN cc_start: 0.7572 (tp40) cc_final: 0.7339 (tp40) REVERT: K 46 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7627 (mmp) REVERT: L 16 ASP cc_start: 0.7685 (p0) cc_final: 0.6993 (p0) REVERT: M 71 VAL cc_start: 0.8652 (m) cc_final: 0.8341 (m) outliers start: 30 outliers final: 18 residues processed: 236 average time/residue: 0.2100 time to fit residues: 76.8344 Evaluate side-chains 174 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain K residue 46 MET Chi-restraints excluded: chain K residue 104 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 40.0000 chunk 112 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 165 optimal weight: 40.0000 chunk 178 optimal weight: 20.0000 chunk 147 optimal weight: 30.0000 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 87 GLN F 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13832 Z= 0.200 Angle : 0.660 7.764 18915 Z= 0.345 Chirality : 0.044 0.139 2418 Planarity : 0.004 0.030 2392 Dihedral : 5.819 29.542 1950 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 1.64 % Allowed : 7.43 % Favored : 90.93 % Cbeta Deviations : 0.00 % 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: -2.98 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -1.77 (0.17), residues: 793 loop : -2.15 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 84 HIS 0.002 0.001 HIS B 50 PHE 0.009 0.002 PHE L 40 TYR 0.022 0.002 TYR A 43 ARG 0.002 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.593 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: A 16 ASP cc_start: 0.7943 (p0) cc_final: 0.7515 (p0) REVERT: A 17 LEU cc_start: 0.8994 (tt) cc_final: 0.8754 (pt) REVERT: B 16 ASP cc_start: 0.8038 (p0) cc_final: 0.7299 (p0) REVERT: C 16 ASP cc_start: 0.7919 (p0) cc_final: 0.7207 (p0) REVERT: C 21 ASP cc_start: 0.8850 (p0) cc_final: 0.8411 (p0) REVERT: D 16 ASP cc_start: 0.8061 (p0) cc_final: 0.7533 (p0) REVERT: D 21 ASP cc_start: 0.8647 (p0) cc_final: 0.8368 (p0) REVERT: E 16 ASP cc_start: 0.7893 (p0) cc_final: 0.7462 (p0) REVERT: E 19 GLN cc_start: 0.7581 (tp40) cc_final: 0.7218 (tp40) REVERT: E 21 ASP cc_start: 0.8760 (p0) cc_final: 0.8443 (p0) REVERT: F 16 ASP cc_start: 0.7796 (p0) cc_final: 0.7162 (p0) REVERT: F 21 ASP cc_start: 0.8729 (p0) cc_final: 0.8253 (p0) REVERT: G 16 ASP cc_start: 0.7828 (p0) cc_final: 0.7230 (p0) REVERT: G 19 GLN cc_start: 0.8006 (tp40) cc_final: 0.7764 (tp40) REVERT: G 21 ASP cc_start: 0.8964 (p0) cc_final: 0.8450 (p0) REVERT: G 23 ASN cc_start: 0.8753 (m-40) cc_final: 0.8294 (m-40) REVERT: H 16 ASP cc_start: 0.7823 (p0) cc_final: 0.7446 (p0) REVERT: I 21 ASP cc_start: 0.8672 (p0) cc_final: 0.8242 (p0) REVERT: I 23 ASN cc_start: 0.8618 (m-40) cc_final: 0.7991 (m-40) REVERT: J 16 ASP cc_start: 0.7564 (p0) cc_final: 0.7150 (p0) REVERT: J 19 GLN cc_start: 0.7112 (tp40) cc_final: 0.6761 (tp40) REVERT: J 23 ASN cc_start: 0.8610 (m-40) cc_final: 0.8005 (m110) REVERT: K 143 MET cc_start: 0.8399 (tmm) cc_final: 0.8186 (tmm) REVERT: L 16 ASP cc_start: 0.7946 (p0) cc_final: 0.7224 (p0) REVERT: L 103 TYR cc_start: 0.7014 (m-80) cc_final: 0.6765 (m-10) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.2032 time to fit residues: 57.1466 Evaluate side-chains 154 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain K residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 79 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 166 optimal weight: 0.0470 chunk 175 optimal weight: 30.0000 chunk 86 optimal weight: 0.0070 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 6.6104 ------------------------------------------------------------------------------- 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: 0.8067 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13832 Z= 0.213 Angle : 0.646 7.408 18915 Z= 0.336 Chirality : 0.043 0.138 2418 Planarity : 0.004 0.034 2392 Dihedral : 5.585 28.860 1950 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 2.24 % Allowed : 8.74 % Favored : 89.02 % Cbeta Deviations : 0.00 % 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: -2.65 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -1.69 (0.20), residues: 650 loop : -1.86 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 84 HIS 0.002 0.001 HIS L 50 PHE 0.011 0.002 PHE K 96 TYR 0.025 0.002 TYR K 43 ARG 0.003 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.586 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: A 16 ASP cc_start: 0.7933 (p0) cc_final: 0.7485 (p0) REVERT: A 17 LEU cc_start: 0.8999 (tt) cc_final: 0.8730 (pt) REVERT: B 16 ASP cc_start: 0.8114 (p0) cc_final: 0.7498 (p0) REVERT: C 16 ASP cc_start: 0.7994 (p0) cc_final: 0.7263 (p0) REVERT: D 16 ASP cc_start: 0.8177 (p0) cc_final: 0.7829 (p0) REVERT: E 16 ASP cc_start: 0.7969 (p0) cc_final: 0.7481 (t0) REVERT: F 16 ASP cc_start: 0.7797 (p0) cc_final: 0.7092 (p0) REVERT: G 16 ASP cc_start: 0.7892 (p0) cc_final: 0.7431 (p0) REVERT: G 21 ASP cc_start: 0.9002 (p0) cc_final: 0.8475 (p0) REVERT: G 23 ASN cc_start: 0.8803 (m-40) cc_final: 0.8365 (m-40) REVERT: H 15 ILE cc_start: 0.3104 (OUTLIER) cc_final: 0.2863 (mt) REVERT: H 16 ASP cc_start: 0.7997 (p0) cc_final: 0.7702 (p0) REVERT: I 23 ASN cc_start: 0.8673 (m-40) cc_final: 0.8384 (m110) REVERT: J 16 ASP cc_start: 0.7584 (p0) cc_final: 0.7219 (p0) REVERT: J 19 GLN cc_start: 0.7092 (tp40) cc_final: 0.6806 (tp40) REVERT: J 23 ASN cc_start: 0.8607 (m-40) cc_final: 0.8050 (m110) REVERT: K 23 ASN cc_start: 0.8663 (m-40) cc_final: 0.8152 (m110) REVERT: K 143 MET cc_start: 0.8424 (tmm) cc_final: 0.8135 (tmm) REVERT: L 16 ASP cc_start: 0.8037 (p0) cc_final: 0.7501 (p0) outliers start: 34 outliers final: 30 residues processed: 168 average time/residue: 0.2043 time to fit residues: 54.0836 Evaluate side-chains 159 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 121 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 12.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 115 GLN ** L 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13832 Z= 0.341 Angle : 0.740 10.610 18915 Z= 0.383 Chirality : 0.044 0.166 2418 Planarity : 0.004 0.038 2392 Dihedral : 6.073 28.863 1950 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.55 % Allowed : 9.14 % Favored : 87.31 % Cbeta Deviations : 0.00 % 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: -2.17 (0.18), residues: 1872 helix: None (None), residues: 0 sheet: -0.49 (0.21), residues: 663 loop : -2.12 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 84 HIS 0.004 0.002 HIS F 50 PHE 0.015 0.003 PHE C 96 TYR 0.016 0.003 TYR L 33 ARG 0.003 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 130 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.4035 (OUTLIER) cc_final: 0.3542 (mt) REVERT: A 16 ASP cc_start: 0.8044 (p0) cc_final: 0.7582 (p0) REVERT: A 17 LEU cc_start: 0.9069 (tt) cc_final: 0.8646 (pt) REVERT: B 16 ASP cc_start: 0.8326 (p0) cc_final: 0.7686 (p0) REVERT: C 15 ILE cc_start: 0.4766 (OUTLIER) cc_final: 0.4213 (mt) REVERT: C 16 ASP cc_start: 0.8185 (p0) cc_final: 0.7626 (p0) REVERT: D 15 ILE cc_start: 0.4543 (OUTLIER) cc_final: 0.4190 (mt) REVERT: D 16 ASP cc_start: 0.8270 (p0) cc_final: 0.7910 (p0) REVERT: D 103 TYR cc_start: 0.7392 (m-10) cc_final: 0.7185 (m-80) REVERT: F 15 ILE cc_start: 0.4585 (OUTLIER) cc_final: 0.3958 (mt) REVERT: F 16 ASP cc_start: 0.8119 (p0) cc_final: 0.7475 (p0) REVERT: G 15 ILE cc_start: 0.5106 (OUTLIER) cc_final: 0.4733 (mt) REVERT: G 16 ASP cc_start: 0.8079 (p0) cc_final: 0.7771 (p0) REVERT: G 19 GLN cc_start: 0.7997 (tp40) cc_final: 0.7738 (tp40) REVERT: G 21 ASP cc_start: 0.8879 (p0) cc_final: 0.8148 (p0) REVERT: G 23 ASN cc_start: 0.8878 (m-40) cc_final: 0.8597 (m-40) REVERT: H 15 ILE cc_start: 0.3827 (OUTLIER) cc_final: 0.3565 (mt) REVERT: H 16 ASP cc_start: 0.8200 (p0) cc_final: 0.7952 (p0) REVERT: I 78 MET cc_start: 0.8602 (mmm) cc_final: 0.7980 (mmm) REVERT: J 15 ILE cc_start: 0.5111 (OUTLIER) cc_final: 0.4749 (mt) REVERT: J 16 ASP cc_start: 0.7746 (p0) cc_final: 0.7404 (p0) REVERT: J 23 ASN cc_start: 0.8724 (m-40) cc_final: 0.8209 (m110) REVERT: K 15 ILE cc_start: 0.4661 (OUTLIER) cc_final: 0.4363 (mt) REVERT: K 16 ASP cc_start: 0.7751 (p0) cc_final: 0.7401 (p0) REVERT: K 23 ASN cc_start: 0.8725 (m-40) cc_final: 0.8301 (m-40) REVERT: L 16 ASP cc_start: 0.8214 (p0) cc_final: 0.7625 (p0) REVERT: M 15 ILE cc_start: 0.5040 (OUTLIER) cc_final: 0.4641 (mt) REVERT: M 23 ASN cc_start: 0.8853 (m-40) cc_final: 0.8468 (m-40) outliers start: 54 outliers final: 31 residues processed: 178 average time/residue: 0.2047 time to fit residues: 57.9292 Evaluate side-chains 158 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 118 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 109 ASN Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 46 MET Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 109 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 30.0000 chunk 158 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 103 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 81 optimal weight: 40.0000 chunk 14 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 87 GLN L 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13832 Z= 0.219 Angle : 0.653 7.708 18915 Z= 0.339 Chirality : 0.043 0.138 2418 Planarity : 0.004 0.037 2392 Dihedral : 5.743 27.167 1950 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.83 % Allowed : 10.39 % Favored : 86.79 % Cbeta Deviations : 0.00 % 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: -1.97 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: -0.23 (0.21), residues: 676 loop : -2.08 (0.16), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 84 HIS 0.001 0.000 HIS L 50 PHE 0.009 0.002 PHE B 96 TYR 0.038 0.002 TYR A 43 ARG 0.003 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 136 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8015 (p0) cc_final: 0.7453 (p0) REVERT: A 17 LEU cc_start: 0.9003 (tt) cc_final: 0.8564 (pt) REVERT: B 16 ASP cc_start: 0.8301 (p0) cc_final: 0.7719 (p0) REVERT: B 87 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: C 15 ILE cc_start: 0.4359 (OUTLIER) cc_final: 0.3870 (mt) REVERT: C 16 ASP cc_start: 0.8100 (p0) cc_final: 0.7591 (p0) REVERT: D 15 ILE cc_start: 0.4384 (OUTLIER) cc_final: 0.3935 (mt) REVERT: F 15 ILE cc_start: 0.4535 (OUTLIER) cc_final: 0.3792 (mt) REVERT: F 16 ASP cc_start: 0.7937 (p0) cc_final: 0.7366 (p0) REVERT: G 15 ILE cc_start: 0.4889 (OUTLIER) cc_final: 0.4278 (mt) REVERT: G 21 ASP cc_start: 0.8911 (p0) cc_final: 0.8232 (p0) REVERT: G 23 ASN cc_start: 0.8865 (m-40) cc_final: 0.8626 (m-40) REVERT: H 16 ASP cc_start: 0.8076 (p0) cc_final: 0.7688 (p0) REVERT: I 78 MET cc_start: 0.8628 (mmm) cc_final: 0.8073 (mmm) REVERT: J 23 ASN cc_start: 0.8721 (m-40) cc_final: 0.8232 (m110) REVERT: J 78 MET cc_start: 0.8798 (mmm) cc_final: 0.8513 (mmm) REVERT: K 15 ILE cc_start: 0.4671 (OUTLIER) cc_final: 0.4415 (mt) REVERT: K 23 ASN cc_start: 0.8695 (m-40) cc_final: 0.8275 (m-40) REVERT: L 16 ASP cc_start: 0.8130 (p0) cc_final: 0.7632 (p0) REVERT: M 23 ASN cc_start: 0.8798 (m-40) cc_final: 0.8449 (m-40) REVERT: M 46 MET cc_start: 0.7622 (mmp) cc_final: 0.7404 (mmp) outliers start: 43 outliers final: 32 residues processed: 169 average time/residue: 0.2176 time to fit residues: 56.4094 Evaluate side-chains 161 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 87 GLN Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 5 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 99 optimal weight: 40.0000 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13832 Z= 0.166 Angle : 0.636 8.674 18915 Z= 0.329 Chirality : 0.043 0.139 2418 Planarity : 0.004 0.033 2392 Dihedral : 5.405 27.991 1950 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.70 % Allowed : 11.05 % Favored : 86.26 % Cbeta Deviations : 0.00 % 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: -1.73 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: -0.02 (0.21), residues: 676 loop : -1.94 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 84 HIS 0.001 0.000 HIS H 50 PHE 0.009 0.002 PHE K 96 TYR 0.028 0.002 TYR C 43 ARG 0.004 0.001 ARG J 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.4451 (OUTLIER) cc_final: 0.3909 (mt) REVERT: A 16 ASP cc_start: 0.7938 (p0) cc_final: 0.7518 (p0) REVERT: A 17 LEU cc_start: 0.8960 (tt) cc_final: 0.8496 (pt) REVERT: B 16 ASP cc_start: 0.8244 (p0) cc_final: 0.7686 (p0) REVERT: B 87 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: C 16 ASP cc_start: 0.8074 (p0) cc_final: 0.7509 (p0) REVERT: C 78 MET cc_start: 0.8610 (mmm) cc_final: 0.8134 (tmm) REVERT: D 15 ILE cc_start: 0.4432 (OUTLIER) cc_final: 0.3848 (mt) REVERT: F 15 ILE cc_start: 0.4315 (OUTLIER) cc_final: 0.3632 (mt) REVERT: F 16 ASP cc_start: 0.7931 (p0) cc_final: 0.7478 (p0) REVERT: G 15 ILE cc_start: 0.4866 (OUTLIER) cc_final: 0.4257 (mt) REVERT: G 21 ASP cc_start: 0.8922 (p0) cc_final: 0.8326 (p0) REVERT: G 23 ASN cc_start: 0.8877 (m-40) cc_final: 0.8442 (m-40) REVERT: H 15 ILE cc_start: 0.3916 (OUTLIER) cc_final: 0.3502 (mt) REVERT: H 16 ASP cc_start: 0.7878 (p0) cc_final: 0.7663 (p0) REVERT: I 78 MET cc_start: 0.8604 (mmm) cc_final: 0.8175 (mmm) REVERT: J 23 ASN cc_start: 0.8699 (m-40) cc_final: 0.8193 (m110) REVERT: K 15 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.4237 (mt) REVERT: K 23 ASN cc_start: 0.8648 (m-40) cc_final: 0.8237 (m-40) REVERT: L 16 ASP cc_start: 0.8106 (p0) cc_final: 0.7618 (p0) outliers start: 41 outliers final: 29 residues processed: 168 average time/residue: 0.2089 time to fit residues: 54.7870 Evaluate side-chains 156 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 30.0000 chunk 70 optimal weight: 40.0000 chunk 104 optimal weight: 0.9980 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 chunk 137 optimal weight: 50.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13832 Z= 0.152 Angle : 0.640 8.903 18915 Z= 0.328 Chirality : 0.042 0.141 2418 Planarity : 0.004 0.032 2392 Dihedral : 5.227 28.157 1950 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.83 % Allowed : 10.91 % Favored : 86.26 % Cbeta Deviations : 0.00 % 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: -1.64 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.07 (0.24), residues: 546 loop : -1.73 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 84 HIS 0.001 0.000 HIS H 50 PHE 0.008 0.002 PHE K 96 TYR 0.037 0.002 TYR F 43 ARG 0.007 0.001 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 130 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.3847 (mt) REVERT: A 16 ASP cc_start: 0.7963 (p0) cc_final: 0.7510 (p0) REVERT: A 17 LEU cc_start: 0.8990 (tt) cc_final: 0.8491 (pt) REVERT: A 23 ASN cc_start: 0.8769 (m-40) cc_final: 0.8566 (m110) REVERT: B 16 ASP cc_start: 0.8204 (p0) cc_final: 0.7695 (p0) REVERT: B 87 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: C 15 ILE cc_start: 0.4160 (OUTLIER) cc_final: 0.3693 (mt) REVERT: C 16 ASP cc_start: 0.8058 (p0) cc_final: 0.7590 (p0) REVERT: D 15 ILE cc_start: 0.4407 (OUTLIER) cc_final: 0.3815 (mt) REVERT: D 23 ASN cc_start: 0.8645 (m-40) cc_final: 0.8402 (m-40) REVERT: F 15 ILE cc_start: 0.4250 (OUTLIER) cc_final: 0.3575 (mt) REVERT: F 16 ASP cc_start: 0.7884 (p0) cc_final: 0.7602 (p0) REVERT: G 21 ASP cc_start: 0.8899 (p0) cc_final: 0.8351 (p0) REVERT: G 23 ASN cc_start: 0.8843 (m-40) cc_final: 0.8417 (m-40) REVERT: H 15 ILE cc_start: 0.4163 (OUTLIER) cc_final: 0.3402 (mt) REVERT: I 78 MET cc_start: 0.8557 (mmm) cc_final: 0.8122 (mmm) REVERT: J 15 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4287 (mt) REVERT: J 23 ASN cc_start: 0.8677 (m-40) cc_final: 0.8165 (m110) REVERT: K 15 ILE cc_start: 0.4493 (OUTLIER) cc_final: 0.4148 (mt) REVERT: K 23 ASN cc_start: 0.8636 (m-40) cc_final: 0.8185 (m110) REVERT: L 16 ASP cc_start: 0.8056 (p0) cc_final: 0.7585 (p0) REVERT: M 15 ILE cc_start: 0.4729 (OUTLIER) cc_final: 0.4396 (mt) outliers start: 43 outliers final: 31 residues processed: 166 average time/residue: 0.2223 time to fit residues: 56.4470 Evaluate side-chains 159 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 134 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 153 optimal weight: 30.0000 chunk 163 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 71 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 162 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13832 Z= 0.181 Angle : 0.648 8.495 18915 Z= 0.332 Chirality : 0.042 0.143 2418 Planarity : 0.004 0.031 2392 Dihedral : 5.242 28.764 1950 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.76 % Allowed : 11.05 % Favored : 86.19 % Cbeta Deviations : 0.00 % 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: -1.52 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.17 (0.22), residues: 663 loop : -1.82 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 84 HIS 0.001 0.000 HIS L 50 PHE 0.017 0.002 PHE G 96 TYR 0.033 0.002 TYR E 43 ARG 0.006 0.001 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.4465 (OUTLIER) cc_final: 0.3903 (mt) REVERT: A 16 ASP cc_start: 0.7972 (p0) cc_final: 0.7536 (p0) REVERT: A 17 LEU cc_start: 0.9001 (tt) cc_final: 0.8462 (pt) REVERT: B 16 ASP cc_start: 0.8266 (p0) cc_final: 0.7755 (p0) REVERT: B 87 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: B 103 TYR cc_start: 0.7392 (m-80) cc_final: 0.7022 (m-10) REVERT: C 15 ILE cc_start: 0.4216 (OUTLIER) cc_final: 0.3760 (mt) REVERT: C 16 ASP cc_start: 0.8134 (p0) cc_final: 0.7675 (p0) REVERT: D 15 ILE cc_start: 0.4702 (OUTLIER) cc_final: 0.4147 (mt) REVERT: D 23 ASN cc_start: 0.8703 (m-40) cc_final: 0.8452 (m-40) REVERT: F 15 ILE cc_start: 0.4241 (OUTLIER) cc_final: 0.3579 (mt) REVERT: F 16 ASP cc_start: 0.7980 (p0) cc_final: 0.7507 (p0) REVERT: F 78 MET cc_start: 0.8288 (tpp) cc_final: 0.7947 (tpp) REVERT: G 21 ASP cc_start: 0.8842 (p0) cc_final: 0.8338 (p0) REVERT: G 23 ASN cc_start: 0.8851 (m-40) cc_final: 0.8425 (m-40) REVERT: H 15 ILE cc_start: 0.3974 (OUTLIER) cc_final: 0.3562 (mt) REVERT: I 15 ILE cc_start: 0.4715 (OUTLIER) cc_final: 0.4207 (mt) REVERT: I 78 MET cc_start: 0.8549 (mmm) cc_final: 0.8135 (mmm) REVERT: J 15 ILE cc_start: 0.5115 (OUTLIER) cc_final: 0.4347 (mt) REVERT: J 23 ASN cc_start: 0.8684 (m-40) cc_final: 0.8179 (m110) REVERT: K 15 ILE cc_start: 0.4466 (OUTLIER) cc_final: 0.4046 (mt) REVERT: K 23 ASN cc_start: 0.8649 (m-40) cc_final: 0.8172 (m-40) REVERT: L 16 ASP cc_start: 0.8088 (p0) cc_final: 0.7612 (p0) REVERT: M 15 ILE cc_start: 0.4945 (OUTLIER) cc_final: 0.4559 (mt) outliers start: 42 outliers final: 31 residues processed: 159 average time/residue: 0.1906 time to fit residues: 49.0281 Evaluate side-chains 161 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 104 SER Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 82 optimal weight: 0.0170 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 88 optimal weight: 30.0000 overall best weight: 10.8028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13832 Z= 0.285 Angle : 0.716 8.866 18915 Z= 0.364 Chirality : 0.043 0.149 2418 Planarity : 0.004 0.031 2392 Dihedral : 5.726 28.786 1950 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 2.70 % Allowed : 11.24 % Favored : 86.06 % Cbeta Deviations : 0.00 % 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: -1.65 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.12 (0.22), residues: 663 loop : -1.93 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 84 HIS 0.003 0.001 HIS L 50 PHE 0.010 0.002 PHE B 96 TYR 0.030 0.003 TYR D 43 ARG 0.006 0.001 ARG B 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.4400 (OUTLIER) cc_final: 0.3937 (mt) REVERT: A 16 ASP cc_start: 0.8092 (p0) cc_final: 0.7677 (p0) REVERT: B 16 ASP cc_start: 0.8419 (p0) cc_final: 0.7871 (p0) REVERT: B 87 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7492 (pm20) REVERT: B 103 TYR cc_start: 0.7408 (m-80) cc_final: 0.7042 (m-10) REVERT: C 15 ILE cc_start: 0.4343 (OUTLIER) cc_final: 0.3944 (mt) REVERT: C 16 ASP cc_start: 0.8203 (p0) cc_final: 0.7730 (p0) REVERT: D 15 ILE cc_start: 0.5107 (OUTLIER) cc_final: 0.4437 (mt) REVERT: D 23 ASN cc_start: 0.8760 (m-40) cc_final: 0.8542 (m-40) REVERT: F 15 ILE cc_start: 0.4549 (OUTLIER) cc_final: 0.4205 (mt) REVERT: F 16 ASP cc_start: 0.8249 (p0) cc_final: 0.7631 (p0) REVERT: F 78 MET cc_start: 0.8245 (tpp) cc_final: 0.7866 (tpp) REVERT: G 15 ILE cc_start: 0.5194 (OUTLIER) cc_final: 0.4540 (mt) REVERT: G 21 ASP cc_start: 0.8921 (p0) cc_final: 0.8366 (p0) REVERT: G 23 ASN cc_start: 0.8945 (m-40) cc_final: 0.8611 (m-40) REVERT: H 15 ILE cc_start: 0.4440 (OUTLIER) cc_final: 0.3892 (mt) REVERT: I 15 ILE cc_start: 0.4881 (OUTLIER) cc_final: 0.4331 (mt) REVERT: I 78 MET cc_start: 0.8627 (mmm) cc_final: 0.8194 (mmm) REVERT: J 15 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.4602 (mt) REVERT: J 23 ASN cc_start: 0.8645 (m-40) cc_final: 0.8170 (m110) REVERT: K 15 ILE cc_start: 0.4725 (OUTLIER) cc_final: 0.4323 (mt) REVERT: K 23 ASN cc_start: 0.8726 (m-40) cc_final: 0.8291 (m-40) REVERT: L 16 ASP cc_start: 0.8083 (p0) cc_final: 0.7623 (p0) REVERT: M 15 ILE cc_start: 0.5177 (OUTLIER) cc_final: 0.4751 (mt) REVERT: M 23 ASN cc_start: 0.8685 (m-40) cc_final: 0.8325 (m-40) outliers start: 41 outliers final: 30 residues processed: 157 average time/residue: 0.2064 time to fit residues: 52.7084 Evaluate side-chains 159 residues out of total 1521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 109 ASN Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 109 ASN Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 46 MET Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain G residue 15 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 134 ASN Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 15 ILE Chi-restraints excluded: chain J residue 6 THR Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 109 ASN Chi-restraints excluded: chain K residue 15 ILE Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain L residue 109 ASN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain M residue 134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 44 optimal weight: 30.0000 chunk 133 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 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 = 0.3184 r_free = 0.3184 target = 0.048203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043324 restraints weight = 98481.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.044301 restraints weight = 62532.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.045019 restraints weight = 43806.201| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13832 Z= 0.210 Angle : 0.677 8.934 18915 Z= 0.345 Chirality : 0.042 0.142 2418 Planarity : 0.004 0.029 2392 Dihedral : 5.547 28.496 1950 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 2.96 % Allowed : 11.51 % Favored : 85.54 % Cbeta Deviations : 0.00 % 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: -1.57 (0.19), residues: 1872 helix: None (None), residues: 0 sheet: 0.19 (0.21), residues: 676 loop : -1.91 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 84 HIS 0.001 0.000 HIS L 50 PHE 0.007 0.002 PHE B 96 TYR 0.026 0.002 TYR F 43 ARG 0.005 0.001 ARG B 44 =============================================================================== Job complete usr+sys time: 2204.69 seconds wall clock time: 41 minutes 57.67 seconds (2517.67 seconds total)