Starting phenix.real_space_refine on Thu Dec 7 21:49:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xyp_10651/12_2023/6xyp_10651.pdb" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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: 3 Type Number sf(0) Gaussians C 3085 2.51 5 N 865 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4955 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "B" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "C" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "D" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "G" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "H" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "I" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "J" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Time building chain proxies: 3.04, per 1000 atoms: 0.61 Number of scatterers: 4955 At special positions: 0 Unit cell: (105.8, 80.5, 41.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1005 8.00 N 865 7.00 C 3085 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.542A pdb=" N VAL A 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 30 removed outlier: 6.717A pdb=" N GLY C 25 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU E 28 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA C 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA E 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 25 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU I 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA I 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.254A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 52 removed outlier: 9.001A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N HIS E 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LYS A 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N VAL I 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS I 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL I 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY A 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU G 46 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY I 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.475A pdb=" N THR C 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN E 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLN I 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU A 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS G 58 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU I 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS G 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL I 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN G 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.365A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.332A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA A 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN I 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR I 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.258A pdb=" N ALA C 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA A 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.496A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 52 removed outlier: 6.880A pdb=" N VAL D 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL F 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY F 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL F 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N HIS F 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL F 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL J 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY J 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N HIS J 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.386A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.284A pdb=" N GLN B 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN F 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR B 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.627A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77 removed outlier: 6.539A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.787A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.278A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 33 through 34 removed outlier: 6.655A pdb=" N THR G 33 " --> pdb=" O LYS I 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 79 hydrogen bonds defined for protein. 237 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: 1.25 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 885 1.28 - 1.35: 775 1.35 - 1.41: 170 1.41 - 1.48: 830 1.48 - 1.54: 2315 Bond restraints: 4975 Sorted by residual: bond pdb=" CB VAL J 37 " pdb=" CG2 VAL J 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.03e+00 bond pdb=" CB VAL F 37 " pdb=" CG2 VAL F 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" CB VAL H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL B 37 " pdb=" CG2 VAL B 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL D 37 " pdb=" CG2 VAL D 37 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 ... (remaining 4970 not shown) Histogram of bond angle deviations from ideal: 106.06 - 111.12: 2301 111.12 - 116.17: 1210 116.17 - 121.22: 1754 121.22 - 126.28: 1445 126.28 - 131.33: 10 Bond angle restraints: 6720 Sorted by residual: angle pdb=" N LYS E 23 " pdb=" CA LYS E 23 " pdb=" C LYS E 23 " ideal model delta sigma weight residual 113.88 110.65 3.23 1.23e+00 6.61e-01 6.89e+00 angle pdb=" N LYS G 23 " pdb=" CA LYS G 23 " pdb=" C LYS G 23 " ideal model delta sigma weight residual 113.88 110.66 3.22 1.23e+00 6.61e-01 6.84e+00 angle pdb=" N LYS I 23 " pdb=" CA LYS I 23 " pdb=" C LYS I 23 " ideal model delta sigma weight residual 113.88 110.67 3.21 1.23e+00 6.61e-01 6.79e+00 angle pdb=" N LYS A 23 " pdb=" CA LYS A 23 " pdb=" C LYS A 23 " ideal model delta sigma weight residual 113.88 110.69 3.19 1.23e+00 6.61e-01 6.75e+00 angle pdb=" N LYS C 23 " pdb=" CA LYS C 23 " pdb=" C LYS C 23 " ideal model delta sigma weight residual 113.88 110.71 3.17 1.23e+00 6.61e-01 6.65e+00 ... (remaining 6715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 2545 13.88 - 27.76: 275 27.76 - 41.63: 50 41.63 - 55.51: 28 55.51 - 69.39: 12 Dihedral angle restraints: 2910 sinusoidal: 965 harmonic: 1945 Sorted by residual: dihedral pdb=" CA ALA I 78 " pdb=" C ALA I 78 " pdb=" N GLN I 79 " pdb=" CA GLN I 79 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA A 78 " pdb=" C ALA A 78 " pdb=" N GLN A 79 " pdb=" CA GLN A 79 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA E 78 " pdb=" C ALA E 78 " pdb=" N GLN E 79 " pdb=" CA GLN E 79 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 580 0.047 - 0.094: 216 0.094 - 0.142: 69 0.142 - 0.189: 0 0.189 - 0.236: 5 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL J 37 " pdb=" CA VAL J 37 " pdb=" CG1 VAL J 37 " pdb=" CG2 VAL J 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL F 37 " pdb=" CA VAL F 37 " pdb=" CG1 VAL F 37 " pdb=" CG2 VAL F 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 867 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.009 2.00e-02 2.50e+03 6.85e-03 8.21e-01 pdb=" CG PHE F 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.009 2.00e-02 2.50e+03 6.77e-03 8.03e-01 pdb=" CG PHE D 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.009 2.00e-02 2.50e+03 6.72e-03 7.91e-01 pdb=" CG PHE B 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 213 2.70 - 3.25: 4728 3.25 - 3.80: 7594 3.80 - 4.35: 9574 4.35 - 4.90: 18788 Nonbonded interactions: 40897 Sorted by model distance: nonbonded pdb=" OE1 GLU C 28 " pdb=" NZ LYS F 60 " model vdw 2.151 2.520 nonbonded pdb=" OE2 GLU A 28 " pdb=" NZ LYS H 60 " model vdw 2.165 2.520 nonbonded pdb=" OE1 GLU A 28 " pdb=" NZ LYS J 60 " model vdw 2.270 2.520 nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLU E 28 " model vdw 2.293 2.520 nonbonded pdb=" NZ LYS H 60 " pdb=" OE1 GLU I 28 " model vdw 2.337 2.520 ... (remaining 40892 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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 individual isotropic 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.460 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.110 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.008 0.047 4975 Z= 0.570 Angle : 0.643 4.284 6720 Z= 0.388 Chirality : 0.055 0.236 870 Planarity : 0.002 0.007 845 Dihedral : 13.985 69.389 1690 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: -5.04 (0.22), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.16), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.015 0.003 PHE F 94 TYR 0.011 0.003 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2381 time to fit residues: 20.6085 Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 50 HIS D 62 GLN F 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4975 Z= 0.136 Angle : 0.435 4.686 6720 Z= 0.243 Chirality : 0.051 0.123 870 Planarity : 0.001 0.007 845 Dihedral : 4.742 15.855 725 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 0.20 % Allowed : 10.82 % Favored : 88.98 % 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: -4.36 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 50 PHE 0.009 0.001 PHE F 94 TYR 0.009 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.2113 time to fit residues: 15.6869 Evaluate side-chains 55 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 52 optimal weight: 0.0030 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 30.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.018 4975 Z= 0.101 Angle : 0.392 4.721 6720 Z= 0.220 Chirality : 0.050 0.123 870 Planarity : 0.001 0.005 845 Dihedral : 4.376 15.958 725 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.41 % Allowed : 13.27 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.88 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 50 PHE 0.006 0.001 PHE F 94 TYR 0.010 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.563 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2081 time to fit residues: 15.5087 Evaluate side-chains 57 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.550 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0481 time to fit residues: 0.8731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 4975 Z= 0.575 Angle : 0.576 6.685 6720 Z= 0.326 Chirality : 0.052 0.122 870 Planarity : 0.002 0.010 845 Dihedral : 5.192 15.590 725 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.24 % Allowed : 13.88 % Favored : 83.88 % 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: -4.03 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 50 PHE 0.018 0.003 PHE F 94 TYR 0.017 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.583 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.2385 time to fit residues: 19.8021 Evaluate side-chains 67 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.536 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0470 time to fit residues: 1.4006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.8006 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4975 Z= 0.235 Angle : 0.445 5.744 6720 Z= 0.249 Chirality : 0.050 0.120 870 Planarity : 0.001 0.007 845 Dihedral : 4.819 15.458 725 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.41 % Allowed : 15.92 % Favored : 83.67 % 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: -3.77 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 50 PHE 0.011 0.001 PHE F 94 TYR 0.011 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.503 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 58 average time/residue: 0.2177 time to fit residues: 15.6030 Evaluate side-chains 59 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.489 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1722 time to fit residues: 1.0688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.0470 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 overall best weight: 5.1684 ------------------------------------------------------------------------------- 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: 0.8043 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4975 Z= 0.427 Angle : 0.521 7.087 6720 Z= 0.291 Chirality : 0.051 0.121 870 Planarity : 0.002 0.009 845 Dihedral : 5.029 15.726 725 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.02 % Allowed : 18.16 % Favored : 80.82 % 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: -3.78 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 50 PHE 0.014 0.002 PHE F 94 TYR 0.015 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.547 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.2413 time to fit residues: 18.2751 Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.495 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0442 time to fit residues: 1.1350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4975 Z= 0.349 Angle : 0.490 6.470 6720 Z= 0.272 Chirality : 0.050 0.123 870 Planarity : 0.002 0.006 845 Dihedral : 4.938 15.906 725 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.61 % Allowed : 19.59 % Favored : 79.80 % 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: -3.72 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 50 PHE 0.013 0.002 PHE F 94 TYR 0.012 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.547 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 0.2336 time to fit residues: 17.3484 Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0483 time to fit residues: 0.9378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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: 0.8020 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4975 Z= 0.305 Angle : 0.474 6.742 6720 Z= 0.263 Chirality : 0.050 0.124 870 Planarity : 0.001 0.008 845 Dihedral : 4.836 15.684 725 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.43 % Allowed : 19.18 % Favored : 79.39 % 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: -3.63 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 50 PHE 0.012 0.002 PHE F 94 TYR 0.013 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.487 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.2243 time to fit residues: 16.6940 Evaluate side-chains 59 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0502 time to fit residues: 1.1320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 4975 Z= 0.537 Angle : 0.583 7.084 6720 Z= 0.324 Chirality : 0.053 0.158 870 Planarity : 0.002 0.007 845 Dihedral : 5.191 15.693 725 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.20 % Allowed : 19.80 % Favored : 80.00 % 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: -3.75 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 50 PHE 0.016 0.003 PHE F 94 TYR 0.015 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.552 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.2540 time to fit residues: 19.5744 Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0464 time to fit residues: 0.8131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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: 0.8024 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4975 Z= 0.316 Angle : 0.496 6.795 6720 Z= 0.271 Chirality : 0.050 0.126 870 Planarity : 0.001 0.008 845 Dihedral : 4.920 15.748 725 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.82 % Allowed : 20.20 % Favored : 78.98 % 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: -3.64 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 50 PHE 0.012 0.002 PHE F 94 TYR 0.013 0.002 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.567 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.2311 time to fit residues: 17.2350 Evaluate side-chains 60 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.535 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0467 time to fit residues: 0.9847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092719 restraints weight = 5480.970| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.79 r_work: 0.3242 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4975 Z= 0.293 Angle : 0.483 6.528 6720 Z= 0.264 Chirality : 0.050 0.125 870 Planarity : 0.001 0.006 845 Dihedral : 4.829 15.623 725 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.41 % Allowed : 20.20 % Favored : 79.39 % 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: -3.56 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 50 PHE 0.012 0.002 PHE F 94 TYR 0.011 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1323.12 seconds wall clock time: 24 minutes 49.01 seconds (1489.01 seconds total)