Starting phenix.real_space_refine on Wed Feb 14 06:09:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zzy_15041/02_2024/7zzy_15041.pdb" } resolution = 3.3 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5600 2.51 5 N 1488 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 36": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8784 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "G" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "E" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "C" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "H" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "B" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "D" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "F" Number of atoms: 1095 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 138, 1087 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain breaks: 2 bond proxies already assigned to first conformer: 1098 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AMET A 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 46 " occ=0.50 residue: pdb=" N AMET G 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET G 46 " occ=0.50 residue: pdb=" N AMET E 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET E 46 " occ=0.50 residue: pdb=" N AMET C 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET C 46 " occ=0.50 residue: pdb=" N AMET H 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET H 46 " occ=0.50 residue: pdb=" N AMET B 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 46 " occ=0.50 residue: pdb=" N AMET D 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET D 46 " occ=0.50 residue: pdb=" N AMET F 46 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET F 46 " occ=0.50 Time building chain proxies: 8.50, per 1000 atoms: 0.97 Number of scatterers: 8784 At special positions: 0 Unit cell: (97.65, 97.65, 80.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1648 8.00 N 1488 7.00 C 5600 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: 3.09 Conformation dependent library (CDL) restraints added in 3.0 seconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2032 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 48.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 28 through 45 removed outlier: 3.584A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.712A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.989A pdb=" N GLN A 119 " --> pdb=" O TRP A 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 Processing helix chain 'G' and resid 28 through 45 removed outlier: 3.577A pdb=" N GLU G 32 " --> pdb=" O GLU G 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG G 44 " --> pdb=" O GLY G 40 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE G 45 " --> pdb=" O MET G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 68 removed outlier: 3.740A pdb=" N ILE G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 119 removed outlier: 3.515A pdb=" N LEU G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN G 119 " --> pdb=" O TRP G 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 Processing helix chain 'E' and resid 28 through 45 removed outlier: 3.594A pdb=" N GLU E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 44 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 45 " --> pdb=" O MET E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 68 removed outlier: 3.742A pdb=" N ILE E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.533A pdb=" N LEU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN E 119 " --> pdb=" O TRP E 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 28 through 45 removed outlier: 3.598A pdb=" N GLU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 45 " --> pdb=" O MET C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 68 removed outlier: 3.724A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.954A pdb=" N GLN C 119 " --> pdb=" O TRP C 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 Processing helix chain 'H' and resid 28 through 45 removed outlier: 3.599A pdb=" N GLU H 32 " --> pdb=" O GLU H 28 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE H 45 " --> pdb=" O MET H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 68 removed outlier: 3.718A pdb=" N ILE H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 119 removed outlier: 3.536A pdb=" N LEU H 108 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN H 119 " --> pdb=" O TRP H 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.593A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 45 " --> pdb=" O MET B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.838A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.537A pdb=" N LEU B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN B 119 " --> pdb=" O TRP B 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 28 through 45 removed outlier: 3.603A pdb=" N GLU D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 45 " --> pdb=" O MET D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.720A pdb=" N ILE D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.536A pdb=" N LEU D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 Processing helix chain 'F' and resid 28 through 45 removed outlier: 3.577A pdb=" N GLU F 32 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 44 " --> pdb=" O GLY F 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 45 " --> pdb=" O MET F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 68 removed outlier: 3.740A pdb=" N ILE F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.551A pdb=" N LEU F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN F 119 " --> pdb=" O TRP F 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 Processing sheet with id=AA2, first strand: chain 'G' and resid 71 through 77 removed outlier: 3.503A pdb=" N ARG G 150 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 71 through 77 Processing sheet with id=AA4, first strand: chain 'C' and resid 71 through 77 Processing sheet with id=AA5, first strand: chain 'H' and resid 71 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 77 Processing sheet with id=AA7, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AA8, first strand: chain 'F' and resid 71 through 77 497 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2881 1.34 - 1.46: 1496 1.46 - 1.58: 4463 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8928 Sorted by residual: bond pdb=" CB PRO F 99 " pdb=" CG PRO F 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.23e-01 bond pdb=" CB PRO B 99 " pdb=" CG PRO B 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.19e-01 bond pdb=" CB PRO E 99 " pdb=" CG PRO E 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.19e-01 bond pdb=" CB PRO H 99 " pdb=" CG PRO H 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.10e-01 bond pdb=" CB PRO D 99 " pdb=" CG PRO D 99 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 4.04e-01 ... (remaining 8923 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 336 106.51 - 113.38: 4988 113.38 - 120.26: 3006 120.26 - 127.13: 3694 127.13 - 134.00: 128 Bond angle restraints: 12152 Sorted by residual: angle pdb=" N GLY C 70 " pdb=" CA GLY C 70 " pdb=" C GLY C 70 " ideal model delta sigma weight residual 111.56 114.39 -2.83 1.01e+00 9.80e-01 7.83e+00 angle pdb=" N GLY G 70 " pdb=" CA GLY G 70 " pdb=" C GLY G 70 " ideal model delta sigma weight residual 111.56 114.32 -2.76 1.01e+00 9.80e-01 7.44e+00 angle pdb=" N GLY F 70 " pdb=" CA GLY F 70 " pdb=" C GLY F 70 " ideal model delta sigma weight residual 111.56 114.31 -2.75 1.01e+00 9.80e-01 7.43e+00 angle pdb=" N GLY D 70 " pdb=" CA GLY D 70 " pdb=" C GLY D 70 " ideal model delta sigma weight residual 110.60 114.27 -3.67 1.46e+00 4.69e-01 6.34e+00 angle pdb=" CA LEU E 76 " pdb=" CB LEU E 76 " pdb=" CG LEU E 76 " ideal model delta sigma weight residual 116.30 123.10 -6.80 3.50e+00 8.16e-02 3.77e+00 ... (remaining 12147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 4697 17.37 - 34.75: 484 34.75 - 52.12: 117 52.12 - 69.50: 25 69.50 - 86.87: 29 Dihedral angle restraints: 5352 sinusoidal: 2200 harmonic: 3152 Sorted by residual: dihedral pdb=" CA BMET G 46 " pdb=" CB BMET G 46 " pdb=" CG BMET G 46 " pdb=" SD BMET G 46 " ideal model delta sinusoidal sigma weight residual 180.00 130.53 49.47 3 1.50e+01 4.44e-03 8.78e+00 dihedral pdb=" CA BMET F 46 " pdb=" CB BMET F 46 " pdb=" CG BMET F 46 " pdb=" SD BMET F 46 " ideal model delta sinusoidal sigma weight residual 180.00 130.60 49.40 3 1.50e+01 4.44e-03 8.77e+00 dihedral pdb=" CB ARG D 35 " pdb=" CG ARG D 35 " pdb=" CD ARG D 35 " pdb=" NE ARG D 35 " ideal model delta sinusoidal sigma weight residual -60.00 -109.12 49.12 3 1.50e+01 4.44e-03 8.73e+00 ... (remaining 5349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 921 0.028 - 0.057: 344 0.057 - 0.085: 78 0.085 - 0.114: 61 0.114 - 0.142: 12 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CG LEU A 63 " pdb=" CB LEU A 63 " pdb=" CD1 LEU A 63 " pdb=" CD2 LEU A 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CG LEU H 63 " pdb=" CB LEU H 63 " pdb=" CD1 LEU H 63 " pdb=" CD2 LEU H 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE E 85 " pdb=" N ILE E 85 " pdb=" C ILE E 85 " pdb=" CB ILE E 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 1413 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 140 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO F 141 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO F 141 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 141 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 140 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO H 141 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO H 141 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO H 141 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 140 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO G 141 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " 0.016 5.00e-02 4.00e+02 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1250 2.77 - 3.30: 7733 3.30 - 3.84: 13861 3.84 - 4.37: 15448 4.37 - 4.90: 28821 Nonbonded interactions: 67113 Sorted by model distance: nonbonded pdb=" OD2 ASP F 80 " pdb=" OG SER F 82 " model vdw 2.238 2.440 nonbonded pdb=" OD2 ASP H 80 " pdb=" OG SER H 82 " model vdw 2.239 2.440 nonbonded pdb=" OD2 ASP B 80 " pdb=" OG SER B 82 " model vdw 2.242 2.440 nonbonded pdb=" OD2 ASP D 80 " pdb=" OG SER D 82 " model vdw 2.243 2.440 nonbonded pdb=" OD2 ASP E 80 " pdb=" OG SER E 82 " model vdw 2.248 2.440 ... (remaining 67108 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' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'B' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'C' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'D' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'E' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'F' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'G' and (resid 6 through 45 or resid 47 through 151)) selection = (chain 'H' and (resid 6 through 45 or resid 47 through 151)) } 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=0.50 max=1.00 mean=0.99 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: 2.050 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: 0.010 Extract box with map and model: 7.000 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.820 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.002 0.025 8928 Z= 0.130 Angle : 0.470 6.800 12152 Z= 0.240 Chirality : 0.036 0.142 1416 Planarity : 0.004 0.030 1552 Dihedral : 16.507 86.874 3320 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1080 helix: 1.91 (0.23), residues: 488 sheet: 0.90 (0.31), residues: 232 loop : -1.09 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 103 HIS 0.001 0.000 HIS C 87 PHE 0.002 0.000 PHE G 10 TYR 0.004 0.001 TYR A 112 ARG 0.002 0.000 ARG G 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2158 time to fit residues: 64.3704 Evaluate side-chains 162 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8928 Z= 0.211 Angle : 0.613 7.083 12152 Z= 0.315 Chirality : 0.039 0.130 1416 Planarity : 0.004 0.028 1552 Dihedral : 3.214 10.180 1192 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.14 % Allowed : 12.29 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1080 helix: 2.16 (0.23), residues: 488 sheet: 1.09 (0.31), residues: 232 loop : -0.99 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 103 HIS 0.001 0.000 HIS C 87 PHE 0.001 0.000 PHE A 13 TYR 0.004 0.001 TYR C 148 ARG 0.001 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.029 Fit side-chains outliers start: 8 outliers final: 0 residues processed: 179 average time/residue: 0.2084 time to fit residues: 51.2060 Evaluate side-chains 151 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8928 Z= 0.214 Angle : 0.698 11.955 12152 Z= 0.358 Chirality : 0.042 0.198 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.725 19.843 1192 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.14 % Allowed : 15.39 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1080 helix: 2.12 (0.23), residues: 488 sheet: 1.04 (0.30), residues: 232 loop : -1.00 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 69 HIS 0.001 0.001 HIS C 87 PHE 0.027 0.003 PHE A 123 TYR 0.016 0.002 TYR H 126 ARG 0.002 0.000 ARG G 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.057 Fit side-chains outliers start: 9 outliers final: 1 residues processed: 161 average time/residue: 0.2133 time to fit residues: 47.0352 Evaluate side-chains 139 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 118 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8928 Z= 0.209 Angle : 0.662 7.701 12152 Z= 0.339 Chirality : 0.042 0.164 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.544 13.784 1192 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.31 % Allowed : 15.70 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1080 helix: 2.24 (0.23), residues: 488 sheet: 1.14 (0.29), residues: 232 loop : -1.11 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 69 HIS 0.002 0.001 HIS D 87 PHE 0.026 0.003 PHE H 123 TYR 0.009 0.001 TYR G 126 ARG 0.005 0.000 ARG D 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 1.008 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.2112 time to fit residues: 45.5726 Evaluate side-chains 146 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 90 optimal weight: 0.0170 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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: 0.7889 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8928 Z= 0.208 Angle : 0.688 7.536 12152 Z= 0.353 Chirality : 0.043 0.212 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.622 12.723 1192 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.21 % Allowed : 17.15 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1080 helix: 2.23 (0.22), residues: 488 sheet: 1.06 (0.29), residues: 232 loop : -1.13 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 69 HIS 0.002 0.001 HIS E 87 PHE 0.020 0.002 PHE H 123 TYR 0.005 0.001 TYR G 148 ARG 0.002 0.000 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.110 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.2081 time to fit residues: 46.6117 Evaluate side-chains 150 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.0060 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8928 Z= 0.227 Angle : 0.684 6.866 12152 Z= 0.350 Chirality : 0.042 0.181 1416 Planarity : 0.004 0.025 1552 Dihedral : 3.538 12.663 1192 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.10 % Allowed : 16.63 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1080 helix: 2.24 (0.23), residues: 488 sheet: 1.14 (0.29), residues: 232 loop : -1.12 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 69 HIS 0.002 0.001 HIS H 87 PHE 0.017 0.002 PHE H 123 TYR 0.004 0.001 TYR H 112 ARG 0.003 0.000 ARG H 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.061 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.2092 time to fit residues: 49.0822 Evaluate side-chains 157 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.0670 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.4980 chunk 56 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN H 15 GLN B 15 GLN D 15 GLN F 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8928 Z= 0.215 Angle : 0.705 8.223 12152 Z= 0.359 Chirality : 0.043 0.203 1416 Planarity : 0.004 0.026 1552 Dihedral : 3.526 12.203 1192 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.10 % Allowed : 18.49 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.25), residues: 1080 helix: 2.30 (0.23), residues: 488 sheet: 1.14 (0.29), residues: 232 loop : -1.05 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS E 87 PHE 0.016 0.002 PHE F 123 TYR 0.004 0.001 TYR F 148 ARG 0.002 0.000 ARG F 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.058 Fit side-chains REVERT: A 131 ASP cc_start: 0.7073 (t0) cc_final: 0.6858 (t0) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.2088 time to fit residues: 46.8284 Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0870 chunk 19 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8928 Z= 0.221 Angle : 0.705 8.077 12152 Z= 0.359 Chirality : 0.043 0.192 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.503 12.173 1192 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 17.98 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1080 helix: 2.35 (0.23), residues: 488 sheet: 1.12 (0.29), residues: 232 loop : -0.99 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS D 87 PHE 0.013 0.002 PHE A 123 TYR 0.002 0.000 TYR F 112 ARG 0.005 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 1.058 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 167 average time/residue: 0.2061 time to fit residues: 47.6014 Evaluate side-chains 155 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.0670 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7909 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8928 Z= 0.234 Angle : 0.724 8.618 12152 Z= 0.367 Chirality : 0.042 0.182 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.491 12.053 1192 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.10 % Allowed : 18.08 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1080 helix: 2.20 (0.22), residues: 488 sheet: 1.04 (0.29), residues: 232 loop : -0.96 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.003 0.001 HIS D 87 PHE 0.012 0.001 PHE H 123 TYR 0.003 0.000 TYR G 126 ARG 0.002 0.000 ARG H 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.058 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.2091 time to fit residues: 45.4266 Evaluate side-chains 156 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 118 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 95 optimal weight: 0.0010 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 65 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.3762 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8928 Z= 0.227 Angle : 0.721 8.669 12152 Z= 0.367 Chirality : 0.041 0.181 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.444 12.385 1192 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 17.98 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1080 helix: 2.20 (0.22), residues: 488 sheet: 1.00 (0.30), residues: 232 loop : -0.89 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 115 HIS 0.002 0.001 HIS E 87 PHE 0.012 0.002 PHE B 123 TYR 0.003 0.000 TYR C 148 ARG 0.002 0.000 ARG G 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2276 time to fit residues: 50.2371 Evaluate side-chains 154 residues out of total 952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.057330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.042581 restraints weight = 171936.026| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 9.85 r_work: 0.2482 rms_B_bonded: 8.98 restraints_weight: 2.0000 r_work: 0.2645 rms_B_bonded: 5.68 restraints_weight: 4.0000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8928 Z= 0.238 Angle : 0.727 9.722 12152 Z= 0.367 Chirality : 0.041 0.199 1416 Planarity : 0.004 0.027 1552 Dihedral : 3.447 12.134 1192 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.21 % Allowed : 18.39 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1080 helix: 2.21 (0.22), residues: 488 sheet: 1.05 (0.30), residues: 232 loop : -0.89 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 69 HIS 0.002 0.001 HIS D 87 PHE 0.011 0.001 PHE F 123 TYR 0.004 0.001 TYR H 148 ARG 0.004 0.000 ARG H 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.73 seconds wall clock time: 39 minutes 54.75 seconds (2394.75 seconds total)