Starting phenix.real_space_refine on Fri Mar 15 14:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/03_2024/6pwe_20506.pdb" } resolution = 3.95 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= 0.004 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 14 5.16 5 C 6576 2.51 5 N 2231 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11923 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 6.45, per 1000 atoms: 0.54 Number of scatterers: 11923 At special positions: 0 Unit cell: (108.36, 113.4, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 294 15.00 O 2808 8.00 N 2231 7.00 C 6576 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: 6.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 59.4% alpha, 1.6% beta 95 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 removed outlier: 3.841A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.602A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.589A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.533A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.853A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.699A pdb=" N ALA C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.700A pdb=" N ALA C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.690A pdb=" N ILE D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.842A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.601A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.590A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.534A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.854A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.698A pdb=" N ALA G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 3.701A pdb=" N ALA G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.689A pdb=" N ILE H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.787A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.109A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.536A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.395A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77 206 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 225 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 95 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1843 1.32 - 1.44: 4466 1.44 - 1.56: 5815 1.56 - 1.68: 586 1.68 - 1.80: 26 Bond restraints: 12736 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.98e+00 bond pdb=" CB PRO A 66 " pdb=" CG PRO A 66 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.09e+00 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.06e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 bond pdb=" C3' DG I 38 " pdb=" O3' DG I 38 " ideal model delta sigma weight residual 1.422 1.373 0.049 3.00e-02 1.11e+03 2.68e+00 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 97.63 - 104.68: 1204 104.68 - 111.72: 6543 111.72 - 118.77: 3699 118.77 - 125.81: 6055 125.81 - 132.85: 960 Bond angle restraints: 18461 Sorted by residual: angle pdb=" C ARG H 30 " pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LYS D 31 " pdb=" CA LYS D 31 " pdb=" CB LYS D 31 " ideal model delta sigma weight residual 110.49 117.07 -6.58 1.69e+00 3.50e-01 1.52e+01 angle pdb=" N LYS H 31 " pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " ideal model delta sigma weight residual 110.49 117.03 -6.54 1.69e+00 3.50e-01 1.50e+01 angle pdb=" C ALA C 102 " pdb=" N GLN C 103 " pdb=" CA GLN C 103 " ideal model delta sigma weight residual 122.46 127.42 -4.96 1.41e+00 5.03e-01 1.24e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.76: 5440 31.76 - 63.52: 1415 63.52 - 95.29: 44 95.29 - 127.05: 0 127.05 - 158.81: 3 Dihedral angle restraints: 6902 sinusoidal: 4744 harmonic: 2158 Sorted by residual: dihedral pdb=" CA LYS D 29 " pdb=" C LYS D 29 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta harmonic sigma weight residual -180.00 -127.05 -52.95 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA LYS H 29 " pdb=" C LYS H 29 " pdb=" N ARG H 30 " pdb=" CA ARG H 30 " ideal model delta harmonic sigma weight residual -180.00 -127.10 -52.90 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ARG D 30 " pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1265 0.044 - 0.088: 667 0.088 - 0.133: 129 0.133 - 0.177: 27 0.177 - 0.221: 10 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CB VAL G 106 " pdb=" CA VAL G 106 " pdb=" CG1 VAL G 106 " pdb=" CG2 VAL G 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL C 106 " pdb=" CA VAL C 106 " pdb=" CG1 VAL C 106 " pdb=" CG2 VAL C 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C 99 " pdb=" CA VAL C 99 " pdb=" CG1 VAL C 99 " pdb=" CG2 VAL C 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2095 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO E 66 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 101 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLY H 101 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY H 101 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2734 2.79 - 3.32: 10074 3.32 - 3.85: 22518 3.85 - 4.37: 26262 4.37 - 4.90: 37230 Nonbonded interactions: 98818 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR H 37 " pdb=" OP1 DG I 48 " model vdw 2.281 2.440 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.317 2.520 nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.318 2.520 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.330 2.496 ... (remaining 98813 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 7.450 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.990 Find NCS groups from input model: 0.430 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.010 0.088 12736 Z= 0.556 Angle : 0.929 8.715 18461 Z= 0.526 Chirality : 0.053 0.221 2098 Planarity : 0.007 0.069 1318 Dihedral : 27.121 158.809 5510 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -6.65 (0.18), residues: 728 helix: -4.66 (0.11), residues: 440 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 106 PHE 0.019 0.003 PHE A 104 TYR 0.018 0.004 TYR F 51 ARG 0.008 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7194 (tt0) cc_final: 0.6709 (tp30) REVERT: B 31 LYS cc_start: 0.8599 (tttt) cc_final: 0.8096 (mptt) REVERT: B 51 TYR cc_start: 0.8455 (m-80) cc_final: 0.7977 (m-80) REVERT: B 79 LYS cc_start: 0.7955 (mttp) cc_final: 0.7747 (mtpt) REVERT: C 109 ASN cc_start: 0.7057 (t0) cc_final: 0.6806 (m-40) REVERT: D 48 ASP cc_start: 0.8152 (p0) cc_final: 0.7794 (p0) REVERT: D 106 HIS cc_start: 0.7772 (m90) cc_final: 0.7565 (m-70) REVERT: E 41 TYR cc_start: 0.8455 (m-80) cc_final: 0.8156 (m-80) REVERT: E 49 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7270 (tpp-160) REVERT: E 118 THR cc_start: 0.9373 (m) cc_final: 0.9075 (p) REVERT: F 80 THR cc_start: 0.8638 (m) cc_final: 0.8278 (p) REVERT: F 84 MET cc_start: 0.6704 (mmm) cc_final: 0.6013 (mmm) REVERT: F 88 TYR cc_start: 0.8433 (m-10) cc_final: 0.7793 (m-80) REVERT: F 98 TYR cc_start: 0.8948 (m-10) cc_final: 0.8633 (m-10) REVERT: H 40 LYS cc_start: 0.9155 (mttt) cc_final: 0.8815 (mtpt) REVERT: H 80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7496 (m-10) REVERT: H 97 LEU cc_start: 0.8873 (mt) cc_final: 0.8648 (mp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3712 time to fit residues: 121.2880 Evaluate side-chains 171 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.0070 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 23 GLN D 60 ASN D 64 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 88 ASN H 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12736 Z= 0.197 Angle : 0.625 5.860 18461 Z= 0.374 Chirality : 0.037 0.179 2098 Planarity : 0.005 0.048 1318 Dihedral : 30.687 160.178 4040 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.85 % Favored : 96.02 % Rotamer: Outliers : 1.62 % Allowed : 14.08 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.23), residues: 728 helix: -3.09 (0.18), residues: 468 sheet: None (None), residues: 0 loop : -3.45 (0.28), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.007 0.001 PHE E 104 TYR 0.015 0.001 TYR C 56 ARG 0.010 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9073 (m-80) cc_final: 0.8836 (m-80) REVERT: A 73 GLU cc_start: 0.7223 (tt0) cc_final: 0.6880 (tp30) REVERT: B 31 LYS cc_start: 0.8858 (tttt) cc_final: 0.8302 (mptt) REVERT: B 88 TYR cc_start: 0.8299 (m-80) cc_final: 0.7621 (m-10) REVERT: C 54 MET cc_start: 0.6654 (mtp) cc_final: 0.6331 (mtm) REVERT: C 109 ASN cc_start: 0.7196 (t0) cc_final: 0.6804 (m-40) REVERT: D 48 ASP cc_start: 0.8126 (p0) cc_final: 0.7635 (p0) REVERT: E 49 ARG cc_start: 0.7555 (mtm180) cc_final: 0.7225 (tpm170) REVERT: F 35 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7881 (mtt-85) REVERT: F 84 MET cc_start: 0.6273 (mmm) cc_final: 0.4718 (tpp) REVERT: F 88 TYR cc_start: 0.8295 (m-10) cc_final: 0.7631 (m-80) REVERT: H 39 TYR cc_start: 0.7777 (t80) cc_final: 0.7482 (t80) REVERT: H 40 LYS cc_start: 0.9136 (mttt) cc_final: 0.8854 (mtpt) REVERT: H 65 ASP cc_start: 0.8655 (t70) cc_final: 0.8260 (t0) REVERT: H 80 TYR cc_start: 0.8068 (m-10) cc_final: 0.7582 (m-10) REVERT: H 98 LEU cc_start: 0.8282 (mp) cc_final: 0.7767 (mp) outliers start: 10 outliers final: 5 residues processed: 213 average time/residue: 0.2980 time to fit residues: 83.7426 Evaluate side-chains 167 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain G residue 100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.2980 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 81 HIS C 93 ASN E 93 GLN F 75 HIS ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12736 Z= 0.327 Angle : 0.671 7.960 18461 Z= 0.389 Chirality : 0.039 0.176 2098 Planarity : 0.005 0.042 1318 Dihedral : 30.854 163.379 4040 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.87 % Favored : 92.99 % Rotamer: Outliers : 5.18 % Allowed : 16.50 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.26), residues: 728 helix: -2.46 (0.21), residues: 452 sheet: None (None), residues: 0 loop : -2.99 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 106 PHE 0.013 0.002 PHE H 62 TYR 0.017 0.002 TYR D 37 ARG 0.005 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7486 (tt0) cc_final: 0.6948 (tp30) REVERT: B 31 LYS cc_start: 0.8756 (tttt) cc_final: 0.8248 (mptt) REVERT: B 88 TYR cc_start: 0.8218 (m-80) cc_final: 0.7478 (m-10) REVERT: C 101 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8737 (mp) REVERT: D 48 ASP cc_start: 0.8367 (p0) cc_final: 0.7942 (p0) REVERT: E 118 THR cc_start: 0.9429 (m) cc_final: 0.9192 (p) REVERT: F 84 MET cc_start: 0.6475 (mmm) cc_final: 0.5414 (tpp) REVERT: F 88 TYR cc_start: 0.8451 (m-10) cc_final: 0.7763 (m-80) REVERT: G 34 ARG cc_start: 0.8425 (ttm170) cc_final: 0.8112 (mtm-85) REVERT: H 54 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8497 (tptm) REVERT: H 80 TYR cc_start: 0.8149 (m-10) cc_final: 0.7755 (m-10) REVERT: H 98 LEU cc_start: 0.8507 (mp) cc_final: 0.8206 (mp) outliers start: 32 outliers final: 20 residues processed: 196 average time/residue: 0.2910 time to fit residues: 76.1852 Evaluate side-chains 180 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 0.0980 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 93 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12736 Z= 0.258 Angle : 0.607 7.787 18461 Z= 0.356 Chirality : 0.036 0.145 2098 Planarity : 0.004 0.038 1318 Dihedral : 30.588 164.488 4040 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.12 % Favored : 95.60 % Rotamer: Outliers : 5.02 % Allowed : 17.64 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.60 (0.27), residues: 728 helix: -1.97 (0.22), residues: 462 sheet: None (None), residues: 0 loop : -2.96 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 106 PHE 0.009 0.001 PHE H 62 TYR 0.022 0.002 TYR B 51 ARG 0.004 0.000 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 169 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7497 (tt0) cc_final: 0.6861 (tp30) REVERT: B 31 LYS cc_start: 0.8547 (tttt) cc_final: 0.8177 (mptt) REVERT: B 88 TYR cc_start: 0.8058 (m-10) cc_final: 0.7437 (m-10) REVERT: D 48 ASP cc_start: 0.8333 (p0) cc_final: 0.7885 (p0) REVERT: E 49 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.6174 (tpm170) REVERT: E 56 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8222 (mtpt) REVERT: F 84 MET cc_start: 0.6502 (mmm) cc_final: 0.5990 (mmm) REVERT: F 88 TYR cc_start: 0.8436 (m-10) cc_final: 0.8218 (m-80) REVERT: H 39 TYR cc_start: 0.7832 (t80) cc_final: 0.7577 (t80) REVERT: H 54 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8454 (tptm) REVERT: H 65 ASP cc_start: 0.8728 (t70) cc_final: 0.8502 (t0) REVERT: H 80 TYR cc_start: 0.8136 (m-10) cc_final: 0.7821 (m-10) REVERT: H 98 LEU cc_start: 0.8612 (mp) cc_final: 0.8295 (mp) outliers start: 31 outliers final: 23 residues processed: 190 average time/residue: 0.2824 time to fit residues: 72.4980 Evaluate side-chains 176 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12736 Z= 0.252 Angle : 0.597 7.452 18461 Z= 0.350 Chirality : 0.036 0.134 2098 Planarity : 0.004 0.036 1318 Dihedral : 30.557 163.676 4040 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.63 % Favored : 94.09 % Rotamer: Outliers : 5.66 % Allowed : 19.42 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.20 (0.28), residues: 728 helix: -1.70 (0.22), residues: 462 sheet: None (None), residues: 0 loop : -2.72 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 106 PHE 0.006 0.001 PHE E 104 TYR 0.011 0.002 TYR D 118 ARG 0.004 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7434 (tt0) cc_final: 0.6844 (tp30) REVERT: B 31 LYS cc_start: 0.8472 (tttt) cc_final: 0.8209 (mptt) REVERT: B 88 TYR cc_start: 0.8015 (m-10) cc_final: 0.7455 (m-10) REVERT: D 48 ASP cc_start: 0.8296 (p0) cc_final: 0.7831 (p0) REVERT: D 77 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8579 (tp) REVERT: E 49 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.6128 (tpm170) REVERT: E 56 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8218 (mtpt) REVERT: F 84 MET cc_start: 0.6492 (mmm) cc_final: 0.5857 (mmm) REVERT: F 88 TYR cc_start: 0.8468 (m-10) cc_final: 0.7882 (m-80) REVERT: G 34 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8610 (ttm-80) REVERT: H 54 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8466 (tptm) REVERT: H 65 ASP cc_start: 0.8710 (t70) cc_final: 0.8503 (t0) REVERT: H 80 TYR cc_start: 0.8067 (m-10) cc_final: 0.7673 (m-10) REVERT: H 98 LEU cc_start: 0.8643 (mp) cc_final: 0.8349 (mp) outliers start: 35 outliers final: 28 residues processed: 181 average time/residue: 0.2673 time to fit residues: 66.2762 Evaluate side-chains 177 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 93 ASN F 25 ASN ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12736 Z= 0.242 Angle : 0.590 9.155 18461 Z= 0.345 Chirality : 0.035 0.133 2098 Planarity : 0.004 0.036 1318 Dihedral : 30.515 162.870 4040 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.67 % Favored : 95.19 % Rotamer: Outliers : 5.50 % Allowed : 21.36 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -2.76 (0.29), residues: 728 helix: -1.33 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.006 0.001 PHE H 62 TYR 0.012 0.001 TYR F 51 ARG 0.003 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7345 (tt0) cc_final: 0.6703 (tp30) REVERT: B 31 LYS cc_start: 0.8417 (tttt) cc_final: 0.8019 (mptt) REVERT: B 59 LYS cc_start: 0.8405 (tttt) cc_final: 0.7802 (tmtt) REVERT: B 88 TYR cc_start: 0.7980 (m-10) cc_final: 0.7455 (m-10) REVERT: D 48 ASP cc_start: 0.8294 (p0) cc_final: 0.7840 (p0) REVERT: E 49 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.6211 (tpm170) REVERT: E 56 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8206 (mtpt) REVERT: F 84 MET cc_start: 0.6384 (mmm) cc_final: 0.5667 (mmm) REVERT: F 88 TYR cc_start: 0.8432 (m-10) cc_final: 0.7889 (m-80) REVERT: G 34 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8646 (ttm-80) REVERT: H 80 TYR cc_start: 0.8077 (m-10) cc_final: 0.7667 (m-10) outliers start: 34 outliers final: 26 residues processed: 176 average time/residue: 0.2824 time to fit residues: 66.9168 Evaluate side-chains 174 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN G 23 GLN G 72 ASN G 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.187 Angle : 0.553 8.727 18461 Z= 0.326 Chirality : 0.033 0.159 2098 Planarity : 0.003 0.035 1318 Dihedral : 30.223 160.085 4040 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.88 % Allowed : 23.62 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.99 (0.30), residues: 728 helix: -0.80 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -2.08 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 106 PHE 0.005 0.001 PHE H 62 TYR 0.009 0.001 TYR D 118 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8429 (mtp-110) cc_final: 0.8076 (ttp80) REVERT: A 62 ILE cc_start: 0.9027 (pt) cc_final: 0.8760 (mt) REVERT: A 73 GLU cc_start: 0.7127 (tt0) cc_final: 0.6500 (tp30) REVERT: B 31 LYS cc_start: 0.8412 (tttt) cc_final: 0.8163 (mptt) REVERT: B 88 TYR cc_start: 0.7882 (m-10) cc_final: 0.7388 (m-10) REVERT: D 48 ASP cc_start: 0.8214 (p0) cc_final: 0.7718 (p0) REVERT: E 49 ARG cc_start: 0.7490 (ttm-80) cc_final: 0.6239 (tpm170) REVERT: E 56 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8195 (mtpt) REVERT: F 84 MET cc_start: 0.6402 (mmm) cc_final: 0.5616 (mmm) REVERT: G 34 ARG cc_start: 0.8848 (ttm-80) cc_final: 0.8492 (mtp85) REVERT: H 56 MET cc_start: 0.7823 (mmm) cc_final: 0.7054 (mtt) REVERT: H 80 TYR cc_start: 0.8072 (m-10) cc_final: 0.7783 (m-10) outliers start: 24 outliers final: 18 residues processed: 173 average time/residue: 0.2820 time to fit residues: 65.7230 Evaluate side-chains 165 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.0670 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.194 Angle : 0.555 7.923 18461 Z= 0.327 Chirality : 0.034 0.135 2098 Planarity : 0.003 0.034 1318 Dihedral : 30.245 160.141 4040 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.75 % Allowed : 25.08 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.67 (0.31), residues: 728 helix: -0.58 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -1.94 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 106 PHE 0.005 0.001 PHE A 67 TYR 0.031 0.002 TYR F 88 ARG 0.003 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.9007 (pt) cc_final: 0.8785 (mt) REVERT: A 73 GLU cc_start: 0.7085 (tt0) cc_final: 0.6485 (tp30) REVERT: B 88 TYR cc_start: 0.7845 (m-10) cc_final: 0.7384 (m-10) REVERT: D 48 ASP cc_start: 0.8227 (p0) cc_final: 0.7884 (p0) REVERT: D 79 HIS cc_start: 0.8244 (t-90) cc_final: 0.7971 (t-90) REVERT: F 84 MET cc_start: 0.6413 (mmm) cc_final: 0.6118 (mmm) REVERT: F 88 TYR cc_start: 0.8840 (m-80) cc_final: 0.8312 (m-80) REVERT: G 34 ARG cc_start: 0.8881 (ttm-80) cc_final: 0.8480 (mtp85) REVERT: H 56 MET cc_start: 0.7891 (mmm) cc_final: 0.7043 (mtt) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.2836 time to fit residues: 62.6971 Evaluate side-chains 158 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 145 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN G 23 GLN G 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12736 Z= 0.225 Angle : 0.568 7.272 18461 Z= 0.333 Chirality : 0.034 0.158 2098 Planarity : 0.003 0.034 1318 Dihedral : 30.324 160.581 4040 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.98 % Favored : 95.74 % Rotamer: Outliers : 3.07 % Allowed : 24.76 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.31), residues: 728 helix: -0.45 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.92 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.005 0.001 PHE E 104 TYR 0.025 0.002 TYR F 88 ARG 0.004 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.7972 (ttp80) REVERT: A 62 ILE cc_start: 0.9016 (pt) cc_final: 0.8795 (mt) REVERT: A 73 GLU cc_start: 0.7099 (tt0) cc_final: 0.6310 (tp30) REVERT: B 88 TYR cc_start: 0.7879 (m-10) cc_final: 0.7353 (m-10) REVERT: D 48 ASP cc_start: 0.8289 (p0) cc_final: 0.7953 (p0) REVERT: D 79 HIS cc_start: 0.8225 (t-90) cc_final: 0.7955 (t-90) REVERT: E 49 ARG cc_start: 0.7386 (ttm-80) cc_final: 0.6201 (tpm170) REVERT: F 84 MET cc_start: 0.6416 (mmm) cc_final: 0.6130 (mmm) REVERT: F 88 TYR cc_start: 0.8872 (m-80) cc_final: 0.8339 (m-80) REVERT: G 34 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.8625 (ttm-80) REVERT: H 56 MET cc_start: 0.8004 (mmm) cc_final: 0.7177 (mtt) outliers start: 19 outliers final: 15 residues processed: 162 average time/residue: 0.2755 time to fit residues: 60.6627 Evaluate side-chains 161 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 93 ASN G 23 GLN G 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12736 Z= 0.223 Angle : 0.571 8.008 18461 Z= 0.334 Chirality : 0.034 0.154 2098 Planarity : 0.003 0.034 1318 Dihedral : 30.323 160.299 4040 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.57 % Favored : 96.15 % Rotamer: Outliers : 3.24 % Allowed : 25.08 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.39 (0.32), residues: 728 helix: -0.37 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.005 0.001 PHE E 104 TYR 0.025 0.002 TYR F 88 ARG 0.004 0.000 ARG D 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.7977 (ttp80) REVERT: A 62 ILE cc_start: 0.8997 (pt) cc_final: 0.8781 (mt) REVERT: A 73 GLU cc_start: 0.7088 (tt0) cc_final: 0.6405 (tp30) REVERT: B 88 TYR cc_start: 0.7914 (m-10) cc_final: 0.7373 (m-10) REVERT: D 48 ASP cc_start: 0.8313 (p0) cc_final: 0.7987 (p0) REVERT: D 79 HIS cc_start: 0.8247 (t-90) cc_final: 0.7989 (t-90) REVERT: F 84 MET cc_start: 0.6410 (mmm) cc_final: 0.6126 (mmm) REVERT: F 88 TYR cc_start: 0.8902 (m-80) cc_final: 0.8396 (m-80) REVERT: G 34 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8463 (mtm-85) REVERT: G 103 GLN cc_start: 0.8637 (pt0) cc_final: 0.8348 (pt0) outliers start: 20 outliers final: 16 residues processed: 160 average time/residue: 0.2709 time to fit residues: 59.1288 Evaluate side-chains 160 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.130950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106883 restraints weight = 24346.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108636 restraints weight = 14847.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109745 restraints weight = 10961.788| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12736 Z= 0.271 Angle : 0.607 10.189 18461 Z= 0.351 Chirality : 0.036 0.162 2098 Planarity : 0.004 0.033 1318 Dihedral : 30.485 161.556 4040 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.92 % Rotamer: Outliers : 3.07 % Allowed : 24.92 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.46 (0.32), residues: 728 helix: -0.41 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 106 PHE 0.006 0.001 PHE H 62 TYR 0.025 0.002 TYR F 51 ARG 0.008 0.001 ARG G 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2120.05 seconds wall clock time: 38 minutes 55.54 seconds (2335.54 seconds total)