Starting phenix.real_space_refine on Thu Dec 7 16:31:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yns_33970/12_2023/7yns_33970.pdb" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1590 2.51 5 N 438 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2526 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 1.66, per 1000 atoms: 0.66 Number of scatterers: 2526 At special positions: 0 Unit cell: (100.43, 107.07, 30.71, 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 498 8.00 N 438 7.00 C 1590 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: 0.93 Conformation dependent library (CDL) restraints added in 543.2 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 45.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 45 through 58 removed outlier: 6.429A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N HIS D 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N VAL C 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N VAL D 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY C 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N THR D 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA D 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LYS D 58 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL C 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL E 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N HIS C 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY E 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 70 through 82 removed outlier: 9.083A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N GLY D 73 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR C 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N THR D 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N GLN D 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 10.534A pdb=" N THR D 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS C 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL C 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR E 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY C 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA E 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN C 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS E 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 86 through 89 removed outlier: 6.924A pdb=" N SER C 87 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 88 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N GLY C 86 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ALA E 89 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE C 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.415A pdb=" N LYS F 45 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL A 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY F 47 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N HIS A 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N VAL F 49 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N VAL A 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY F 51 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N THR A 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA F 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N ALA A 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL F 55 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS A 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU F 57 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL F 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS F 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLY B 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 82 removed outlier: 9.089A pdb=" N VAL F 70 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.338A pdb=" N GLY A 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR F 72 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N THR A 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 74 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL A 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ALA F 76 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLN A 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR A 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N LYS F 80 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY F 73 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL F 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 78 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN F 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS B 80 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR F 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 82 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 89 removed outlier: 6.935A pdb=" N SER F 87 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 88 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N GLY F 86 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ALA B 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE F 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) 26 hydrogen bonds defined for protein. 78 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: 0.56 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 432 1.29 - 1.35: 390 1.35 - 1.41: 102 1.41 - 1.48: 421 1.48 - 1.54: 1193 Bond restraints: 2538 Sorted by residual: bond pdb=" CB THR D 75 " pdb=" CG2 THR D 75 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.28e+00 bond pdb=" CB THR F 75 " pdb=" CG2 THR F 75 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB THR A 75 " pdb=" CG2 THR A 75 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB THR C 75 " pdb=" CG2 THR C 75 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB THR B 75 " pdb=" CG2 THR B 75 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 ... (remaining 2533 not shown) Histogram of bond angle deviations from ideal: 106.09 - 111.09: 1121 111.09 - 116.09: 698 116.09 - 121.09: 833 121.09 - 126.08: 774 126.08 - 131.08: 6 Bond angle restraints: 3432 Sorted by residual: angle pdb=" N GLY F 67 " pdb=" CA GLY F 67 " pdb=" C GLY F 67 " ideal model delta sigma weight residual 114.76 117.58 -2.82 1.70e+00 3.46e-01 2.76e+00 angle pdb=" N GLY D 67 " pdb=" CA GLY D 67 " pdb=" C GLY D 67 " ideal model delta sigma weight residual 114.76 117.57 -2.81 1.70e+00 3.46e-01 2.74e+00 angle pdb=" N GLY B 67 " pdb=" CA GLY B 67 " pdb=" C GLY B 67 " ideal model delta sigma weight residual 114.76 117.57 -2.81 1.70e+00 3.46e-01 2.72e+00 angle pdb=" N GLY E 67 " pdb=" CA GLY E 67 " pdb=" C GLY E 67 " ideal model delta sigma weight residual 114.76 117.56 -2.80 1.70e+00 3.46e-01 2.72e+00 angle pdb=" N GLY A 67 " pdb=" CA GLY A 67 " pdb=" C GLY A 67 " ideal model delta sigma weight residual 115.08 117.61 -2.53 1.54e+00 4.22e-01 2.71e+00 ... (remaining 3427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.16: 1116 8.16 - 16.31: 252 16.31 - 24.47: 78 24.47 - 32.62: 18 32.62 - 40.78: 18 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA LYS D 80 " pdb=" CB LYS D 80 " pdb=" CG LYS D 80 " pdb=" CD LYS D 80 " ideal model delta sinusoidal sigma weight residual 180.00 139.22 40.78 3 1.50e+01 4.44e-03 7.28e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual 180.00 139.25 40.75 3 1.50e+01 4.44e-03 7.27e+00 dihedral pdb=" CA LYS E 80 " pdb=" CB LYS E 80 " pdb=" CG LYS E 80 " pdb=" CD LYS E 80 " ideal model delta sinusoidal sigma weight residual 180.00 139.27 40.73 3 1.50e+01 4.44e-03 7.27e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 202 0.037 - 0.073: 142 0.073 - 0.110: 86 0.110 - 0.146: 20 0.146 - 0.183: 6 Chirality restraints: 456 Sorted by residual: chirality pdb=" CB THR C 75 " pdb=" CA THR C 75 " pdb=" OG1 THR C 75 " pdb=" CG2 THR C 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CB THR D 75 " pdb=" CA THR D 75 " pdb=" OG1 THR D 75 " pdb=" CG2 THR D 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" CB THR E 75 " pdb=" CA THR E 75 " pdb=" OG1 THR E 75 " pdb=" CG2 THR E 75 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 453 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 94 " 0.009 2.00e-02 2.50e+03 8.26e-03 1.19e+00 pdb=" CG PHE E 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE E 94 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE E 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE E 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 94 " 0.003 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 8.21e-03 1.18e+00 pdb=" CG PHE B 94 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " 0.009 2.00e-02 2.50e+03 8.21e-03 1.18e+00 pdb=" CG PHE C 94 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " 0.003 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 303 2.77 - 3.30: 2398 3.30 - 3.83: 3803 3.83 - 4.37: 4190 4.37 - 4.90: 9044 Nonbonded interactions: 19738 Sorted by model distance: nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS C 80 " model vdw 2.233 2.520 nonbonded pdb=" OE1 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.234 2.520 nonbonded pdb=" OE1 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.234 2.520 nonbonded pdb=" OE1 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.234 2.520 nonbonded pdb=" OE1 GLU F 46 " pdb=" NZ LYS F 80 " model vdw 2.234 2.520 ... (remaining 19733 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' } 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: 1.950 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: 8.970 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.009 0.037 2538 Z= 0.607 Angle : 0.656 2.987 3432 Z= 0.377 Chirality : 0.061 0.183 456 Planarity : 0.003 0.008 420 Dihedral : 11.512 40.779 858 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: -3.28 (0.33), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.25), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS B 50 PHE 0.019 0.006 PHE E 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.3520 time to fit residues: 42.9670 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2538 Z= 0.157 Angle : 0.474 3.607 3432 Z= 0.273 Chirality : 0.053 0.132 456 Planarity : 0.002 0.014 420 Dihedral : 4.166 10.899 366 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.78 % Allowed : 10.47 % Favored : 88.76 % 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: -2.59 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 50 PHE 0.027 0.007 PHE E 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.279 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 1.0243 time to fit residues: 33.8501 Evaluate side-chains 16 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 2538 Z= 0.408 Angle : 0.565 2.984 3432 Z= 0.329 Chirality : 0.055 0.133 456 Planarity : 0.002 0.012 420 Dihedral : 4.673 13.630 366 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.71 % Allowed : 15.50 % Favored : 81.78 % 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: -2.58 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS C 50 PHE 0.028 0.004 PHE A 94 TYR 0.007 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 17 time to evaluate : 0.288 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 20 average time/residue: 0.3564 time to fit residues: 7.9780 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 17 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.0249 time to fit residues: 0.5084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2538 Z= 0.213 Angle : 0.457 2.817 3432 Z= 0.267 Chirality : 0.052 0.132 456 Planarity : 0.002 0.013 420 Dihedral : 4.285 13.489 366 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.71 % Allowed : 15.89 % Favored : 81.40 % 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: -2.32 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 50 PHE 0.030 0.007 PHE E 94 TYR 0.006 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.271 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 23 average time/residue: 0.6195 time to fit residues: 15.1702 Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 5 average time/residue: 0.0594 time to fit residues: 0.7777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 2538 Z= 0.479 Angle : 0.589 3.041 3432 Z= 0.344 Chirality : 0.055 0.133 456 Planarity : 0.002 0.014 420 Dihedral : 4.764 14.638 366 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.10 % Allowed : 17.05 % Favored : 79.84 % 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: -2.40 (0.39), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.032 0.007 PHE C 94 TYR 0.008 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 18 time to evaluate : 0.285 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 20 average time/residue: 0.3457 time to fit residues: 7.7511 Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 18 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 1 residues processed: 5 average time/residue: 0.0265 time to fit residues: 0.5784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.8330 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2538 Z= 0.185 Angle : 0.444 2.975 3432 Z= 0.261 Chirality : 0.052 0.132 456 Planarity : 0.002 0.014 420 Dihedral : 4.204 14.210 366 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.55 % Allowed : 17.83 % Favored : 80.62 % 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 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.033 0.009 PHE B 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.280 Fit side-chains outliers start: 4 outliers final: 5 residues processed: 20 average time/residue: 0.3436 time to fit residues: 7.6965 Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 0.0628 time to fit residues: 0.6734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 2538 Z= 0.486 Angle : 0.593 3.237 3432 Z= 0.347 Chirality : 0.056 0.132 456 Planarity : 0.003 0.015 420 Dihedral : 4.743 13.917 366 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.26 % Allowed : 15.89 % Favored : 79.84 % 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: -2.29 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.035 0.008 PHE B 94 TYR 0.007 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 0.285 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 26 average time/residue: 0.8419 time to fit residues: 22.8981 Evaluate side-chains 30 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 22 time to evaluate : 0.251 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 1 residues processed: 7 average time/residue: 0.0257 time to fit residues: 0.6496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8308 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2538 Z= 0.182 Angle : 0.502 5.446 3432 Z= 0.293 Chirality : 0.052 0.129 456 Planarity : 0.003 0.018 420 Dihedral : 4.139 14.881 366 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.55 % Allowed : 18.99 % Favored : 79.46 % 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: -2.08 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS F 50 PHE 0.035 0.010 PHE B 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.296 Fit side-chains outliers start: 4 outliers final: 5 residues processed: 24 average time/residue: 0.6101 time to fit residues: 15.5869 Evaluate side-chains 25 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 0.0657 time to fit residues: 0.7023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2538 Z= 0.224 Angle : 0.532 5.576 3432 Z= 0.309 Chirality : 0.052 0.128 456 Planarity : 0.003 0.017 420 Dihedral : 4.185 14.340 366 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 19.38 % Favored : 79.07 % 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: -2.06 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.035 0.010 PHE E 94 TYR 0.005 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.291 Fit side-chains outliers start: 4 outliers final: 5 residues processed: 21 average time/residue: 0.3703 time to fit residues: 8.6936 Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 4 average time/residue: 0.0611 time to fit residues: 0.6627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0170 chunk 29 optimal weight: 7.9990 overall best weight: 3.5024 ------------------------------------------------------------------------------- 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: 0.8367 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2538 Z= 0.418 Angle : 0.650 5.915 3432 Z= 0.374 Chirality : 0.054 0.133 456 Planarity : 0.003 0.016 420 Dihedral : 4.683 16.799 366 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.55 % Allowed : 19.38 % Favored : 79.07 % 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: -2.16 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS C 50 PHE 0.034 0.010 PHE E 94 TYR 0.006 0.001 TYR F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.275 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 20 average time/residue: 0.3478 time to fit residues: 7.8000 Evaluate side-chains 22 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.285 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 3 average time/residue: 0.0765 time to fit residues: 0.6568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.170326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139102 restraints weight = 3075.909| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.59 r_work: 0.3818 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2538 Z= 0.345 Angle : 0.612 6.085 3432 Z= 0.353 Chirality : 0.053 0.133 456 Planarity : 0.003 0.017 420 Dihedral : 4.555 16.010 366 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.78 % Allowed : 20.16 % Favored : 79.07 % 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: -2.14 (0.41), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.036 0.010 PHE B 94 TYR 0.006 0.001 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1207.53 seconds wall clock time: 22 minutes 35.32 seconds (1355.32 seconds total)