Starting phenix.real_space_refine on Sat Jul 20 12:01:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8whb_37538/07_2024/8whb_37538.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 268 5.49 5 S 12 5.16 5 C 6211 2.51 5 N 2067 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11176 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 733 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 621 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2729 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Chain: "J" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2765 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Time building chain proxies: 6.11, per 1000 atoms: 0.55 Number of scatterers: 11176 At special positions: 0 Unit cell: (118.845, 101.745, 127.395, 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 12 16.00 P 268 15.00 O 2618 8.00 N 2067 7.00 C 6211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.58 Conformation dependent library (CDL) restraints added in 980.6 milliseconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 74.4% alpha, 3.3% beta 86 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.668A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.747A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.697A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.909A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.966A pdb=" N LEU C 117 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.736A pdb=" N ASN D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.732A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.743A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.606A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.586A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.791A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.804A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.871A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.689A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.452A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.602A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.786A pdb=" N ASN H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 127 removed outlier: 3.879A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.667A pdb=" N ALA H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.545A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 7.000A pdb=" N THR B 96 " --> pdb=" O THR C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.449A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.609A pdb=" N THR F 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.158A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 359 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 6.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1313 1.32 - 1.44: 4203 1.44 - 1.56: 5846 1.56 - 1.68: 537 1.68 - 1.80: 22 Bond restraints: 11921 Sorted by residual: bond pdb=" N GLU F 52 " pdb=" CA GLU F 52 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" NE ARG C 89 " pdb=" CZ ARG C 89 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N GLN F 27 " pdb=" CA GLN F 27 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.35e-02 5.49e+03 1.02e+01 bond pdb=" N LYS F 59 " pdb=" CA LYS F 59 " ideal model delta sigma weight residual 1.459 1.499 -0.041 1.28e-02 6.10e+03 1.01e+01 ... (remaining 11916 not shown) Histogram of bond angle deviations from ideal: 97.99 - 104.90: 1086 104.90 - 111.81: 6240 111.81 - 118.72: 3423 118.72 - 125.64: 5612 125.64 - 132.55: 886 Bond angle restraints: 17247 Sorted by residual: angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 111.50 125.48 -13.98 1.50e+00 4.44e-01 8.69e+01 angle pdb=" N THR E 107 " pdb=" CA THR E 107 " pdb=" C THR E 107 " ideal model delta sigma weight residual 113.18 102.29 10.89 1.21e+00 6.83e-01 8.10e+01 angle pdb=" O3' DA I 106 " pdb=" C3' DA I 106 " pdb=" C2' DA I 106 " ideal model delta sigma weight residual 111.50 124.99 -13.49 1.50e+00 4.44e-01 8.09e+01 angle pdb=" O3' DG I 126 " pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 111.50 124.43 -12.93 1.50e+00 4.44e-01 7.43e+01 angle pdb=" O3' DT J 24 " pdb=" C3' DT J 24 " pdb=" C2' DT J 24 " ideal model delta sigma weight residual 111.50 124.43 -12.93 1.50e+00 4.44e-01 7.43e+01 ... (remaining 17242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5232 34.91 - 69.82: 1200 69.82 - 104.74: 34 104.74 - 139.65: 2 139.65 - 174.56: 4 Dihedral angle restraints: 6472 sinusoidal: 4381 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLU H 118 " pdb=" C GLU H 118 " pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU E 133 " pdb=" C GLU E 133 " pdb=" N ARG E 134 " pdb=" CA ARG E 134 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1955 0.164 - 0.329: 12 0.329 - 0.493: 0 0.493 - 0.657: 2 0.657 - 0.821: 3 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.66 -1.84 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C3' DA I 106 " pdb=" C4' DA I 106 " pdb=" O3' DA I 106 " pdb=" C2' DA I 106 " both_signs ideal model delta sigma weight residual False -2.66 -1.94 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3' DT J 24 " pdb=" C4' DT J 24 " pdb=" O3' DT J 24 " pdb=" C2' DT J 24 " both_signs ideal model delta sigma weight residual False -2.66 -1.98 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 1969 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.045 2.00e-02 2.50e+03 2.09e-02 9.82e+00 pdb=" N1 DC J 27 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 106 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ASP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP E 106 " -0.019 2.00e-02 2.50e+03 pdb=" N THR E 107 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 51 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C TYR F 51 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR F 51 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 52 " -0.018 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2427 2.80 - 3.32: 9588 3.32 - 3.85: 20983 3.85 - 4.37: 25240 4.37 - 4.90: 35944 Nonbonded interactions: 94182 Sorted by model distance: nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.272 2.440 nonbonded pdb=" OH TYR G 58 " pdb=" OE2 GLU G 62 " model vdw 2.335 2.440 nonbonded pdb=" NE ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.342 2.520 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 96 " model vdw 2.415 2.440 nonbonded pdb=" NH2 ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.420 2.520 ... (remaining 94177 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' and resid 43 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 18 through 110) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.630 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 11921 Z= 0.428 Angle : 1.006 13.981 17247 Z= 0.640 Chirality : 0.060 0.821 1972 Planarity : 0.006 0.055 1249 Dihedral : 27.902 174.559 5120 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.29), residues: 707 helix: -0.87 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.40 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 83 PHE 0.049 0.003 PHE C 26 TYR 0.013 0.003 TYR H 65 ARG 0.010 0.001 ARG G 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.939 Fit side-chains REVERT: C 105 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0) REVERT: C 111 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (p0) REVERT: D 111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8191 (mtpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4223 time to fit residues: 105.2173 Evaluate side-chains 152 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 85 GLN H 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11921 Z= 0.245 Angle : 0.641 8.483 17247 Z= 0.378 Chirality : 0.039 0.267 1972 Planarity : 0.005 0.046 1249 Dihedral : 31.036 176.811 3713 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.35 % Allowed : 10.57 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.32), residues: 707 helix: 0.83 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.06 (0.39), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.016 0.001 PHE C 26 TYR 0.008 0.001 TYR A 54 ARG 0.004 0.001 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 0.940 Fit side-chains REVERT: C 18 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7966 (mpp80) REVERT: C 74 ASN cc_start: 0.7317 (m-40) cc_final: 0.6830 (t0) REVERT: C 105 ASN cc_start: 0.8832 (t0) cc_final: 0.8075 (t0) REVERT: C 111 ASN cc_start: 0.8050 (t0) cc_final: 0.7796 (p0) REVERT: D 104 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7577 (mptt) REVERT: D 111 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8225 (mtpt) REVERT: D 141 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8454 (ttpp) REVERT: F 44 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8456 (mtmt) REVERT: F 79 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8570 (mtmt) REVERT: H 104 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7972 (ttmm) outliers start: 14 outliers final: 5 residues processed: 170 average time/residue: 0.3607 time to fit residues: 76.8955 Evaluate side-chains 158 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 GLN F 75 HIS H 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 11921 Z= 0.529 Angle : 0.733 9.448 17247 Z= 0.425 Chirality : 0.046 0.206 1972 Planarity : 0.005 0.046 1249 Dihedral : 31.293 176.777 3713 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.03 % Allowed : 11.41 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.31), residues: 707 helix: 1.12 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.026 0.002 PHE C 26 TYR 0.011 0.002 TYR B 51 ARG 0.004 0.001 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 0.774 Fit side-chains REVERT: C 18 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8875 (mtm180) REVERT: C 74 ASN cc_start: 0.8261 (m-40) cc_final: 0.7840 (t0) REVERT: C 105 ASN cc_start: 0.8904 (t0) cc_final: 0.8101 (t0) REVERT: D 101 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7693 (tp30) REVERT: D 111 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8503 (mtpt) REVERT: F 44 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8459 (mtmt) REVERT: F 79 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8617 (mtmt) REVERT: H 68 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8848 (mtpt) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 0.3579 time to fit residues: 77.6344 Evaluate side-chains 166 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11921 Z= 0.210 Angle : 0.565 6.967 17247 Z= 0.338 Chirality : 0.035 0.156 1972 Planarity : 0.004 0.038 1249 Dihedral : 30.835 176.841 3713 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.85 % Allowed : 12.58 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.33), residues: 707 helix: 1.85 (0.24), residues: 525 sheet: None (None), residues: 0 loop : -1.94 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.011 0.001 PHE C 26 TYR 0.007 0.001 TYR H 65 ARG 0.003 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 0.914 Fit side-chains REVERT: C 18 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8321 (mpp80) REVERT: C 21 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8960 (ttmm) REVERT: C 74 ASN cc_start: 0.7881 (m-40) cc_final: 0.7569 (t0) REVERT: C 105 ASN cc_start: 0.8821 (t0) cc_final: 0.8195 (t0) REVERT: E 77 ASP cc_start: 0.7975 (m-30) cc_final: 0.7771 (m-30) REVERT: F 44 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (mtmt) REVERT: F 79 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8613 (mtmt) REVERT: G 75 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8842 (mmtm) REVERT: G 78 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8498 (mtp85) REVERT: H 68 LYS cc_start: 0.9286 (ttmt) cc_final: 0.8867 (mttt) REVERT: H 104 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8030 (ttmm) outliers start: 17 outliers final: 7 residues processed: 155 average time/residue: 0.3638 time to fit residues: 70.9586 Evaluate side-chains 151 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11921 Z= 0.237 Angle : 0.566 7.277 17247 Z= 0.336 Chirality : 0.035 0.132 1972 Planarity : 0.004 0.036 1249 Dihedral : 30.622 177.223 3713 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 15.44 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.33), residues: 707 helix: 2.19 (0.23), residues: 520 sheet: None (None), residues: 0 loop : -1.71 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.013 0.001 PHE C 26 TYR 0.009 0.001 TYR B 51 ARG 0.004 0.000 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8679 (pp20) cc_final: 0.8422 (pm20) REVERT: C 18 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8286 (mpp80) REVERT: C 74 ASN cc_start: 0.7869 (m-40) cc_final: 0.7602 (t0) REVERT: C 95 SER cc_start: 0.9282 (p) cc_final: 0.9018 (p) REVERT: C 105 ASN cc_start: 0.8917 (t0) cc_final: 0.8163 (t0) REVERT: C 109 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7353 (mtm) REVERT: F 44 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (mtmt) REVERT: F 79 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8604 (mtmt) REVERT: H 68 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8905 (mttt) REVERT: H 104 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8138 (ttmm) outliers start: 11 outliers final: 5 residues processed: 156 average time/residue: 0.3479 time to fit residues: 68.8970 Evaluate side-chains 157 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8465 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11921 Z= 0.228 Angle : 0.549 7.017 17247 Z= 0.327 Chirality : 0.034 0.128 1972 Planarity : 0.004 0.036 1249 Dihedral : 30.349 177.664 3713 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.85 % Allowed : 16.44 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.33), residues: 707 helix: 2.36 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.56 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.014 0.001 PHE C 26 TYR 0.007 0.001 TYR B 51 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.917 Fit side-chains REVERT: A 59 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: C 18 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8207 (mpp80) REVERT: C 74 ASN cc_start: 0.7894 (m-40) cc_final: 0.7644 (t0) REVERT: C 105 ASN cc_start: 0.8905 (t0) cc_final: 0.8135 (t0) REVERT: F 44 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8354 (mtmt) REVERT: F 79 LYS cc_start: 0.8847 (mtpt) cc_final: 0.8614 (mtmt) REVERT: H 68 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8892 (mttt) outliers start: 17 outliers final: 8 residues processed: 156 average time/residue: 0.3688 time to fit residues: 72.2554 Evaluate side-chains 159 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11921 Z= 0.181 Angle : 0.546 7.063 17247 Z= 0.325 Chirality : 0.033 0.130 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.351 177.748 3713 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.85 % Allowed : 16.61 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.33), residues: 707 helix: 2.45 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR F 98 ARG 0.003 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 0.906 Fit side-chains REVERT: A 59 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8480 (pm20) REVERT: C 18 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8213 (mpp80) REVERT: C 74 ASN cc_start: 0.7808 (m-40) cc_final: 0.7557 (t0) REVERT: C 105 ASN cc_start: 0.8899 (t0) cc_final: 0.8114 (t0) REVERT: F 44 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8342 (mtmt) REVERT: F 79 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8590 (mtmt) REVERT: H 68 LYS cc_start: 0.9262 (ttmt) cc_final: 0.8889 (mttt) outliers start: 11 outliers final: 8 residues processed: 152 average time/residue: 0.3527 time to fit residues: 68.1010 Evaluate side-chains 158 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0020 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11921 Z= 0.216 Angle : 0.546 7.093 17247 Z= 0.324 Chirality : 0.034 0.133 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.310 178.292 3713 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.18 % Allowed : 16.78 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.33), residues: 707 helix: 2.53 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.53 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.012 0.001 PHE C 26 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.998 Fit side-chains REVERT: A 97 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: C 18 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8298 (mpp80) REVERT: C 74 ASN cc_start: 0.7808 (m-40) cc_final: 0.7593 (t0) REVERT: C 105 ASN cc_start: 0.8900 (t0) cc_final: 0.8081 (t0) REVERT: F 44 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8417 (mtmt) REVERT: F 79 LYS cc_start: 0.8819 (mtpt) cc_final: 0.8591 (mtmt) REVERT: H 68 LYS cc_start: 0.9227 (ttmt) cc_final: 0.8864 (mttt) outliers start: 13 outliers final: 8 residues processed: 153 average time/residue: 0.3480 time to fit residues: 67.6149 Evaluate side-chains 156 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8544 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11921 Z= 0.353 Angle : 0.612 7.422 17247 Z= 0.358 Chirality : 0.038 0.155 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.442 178.327 3713 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.85 % Allowed : 15.77 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.32), residues: 707 helix: 2.33 (0.23), residues: 517 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.016 0.002 PHE C 26 TYR 0.010 0.001 TYR A 54 ARG 0.003 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.810 Fit side-chains REVERT: A 59 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: C 18 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8906 (mmm-85) REVERT: C 74 ASN cc_start: 0.8211 (m-40) cc_final: 0.7941 (t0) REVERT: C 105 ASN cc_start: 0.8894 (t0) cc_final: 0.8078 (t0) REVERT: F 44 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8560 (mtmt) REVERT: F 79 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8625 (mtmt) REVERT: H 68 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8895 (mttt) outliers start: 17 outliers final: 9 residues processed: 152 average time/residue: 0.3780 time to fit residues: 72.4904 Evaluate side-chains 156 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11921 Z= 0.192 Angle : 0.571 7.045 17247 Z= 0.338 Chirality : 0.035 0.153 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.368 178.339 3713 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 17.11 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.33), residues: 707 helix: 2.45 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 134 PHE 0.012 0.001 PHE A 67 TYR 0.014 0.001 TYR B 88 ARG 0.004 0.000 ARG C 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 144 time to evaluate : 0.942 Fit side-chains REVERT: A 59 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: C 18 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8899 (mmm-85) REVERT: C 74 ASN cc_start: 0.8133 (m-40) cc_final: 0.7884 (t0) REVERT: C 105 ASN cc_start: 0.8877 (t0) cc_final: 0.8076 (t0) REVERT: F 44 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8541 (mtmt) REVERT: F 79 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8605 (mtmt) REVERT: G 109 MET cc_start: 0.6483 (mtm) cc_final: 0.6223 (mtt) REVERT: H 68 LYS cc_start: 0.9263 (ttmt) cc_final: 0.8897 (mttt) outliers start: 10 outliers final: 7 residues processed: 148 average time/residue: 0.3518 time to fit residues: 65.8075 Evaluate side-chains 152 residues out of total 596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain H residue 76 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 31 optimal weight: 0.0570 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.9102 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.109867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.073452 restraints weight = 20604.046| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.66 r_work: 0.2715 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11921 Z= 0.206 Angle : 0.563 7.939 17247 Z= 0.332 Chirality : 0.034 0.150 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.264 178.535 3713 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.85 % Allowed : 17.11 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.33), residues: 707 helix: 2.50 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.45 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.014 0.001 TYR F 98 ARG 0.003 0.000 ARG C 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2493.12 seconds wall clock time: 44 minutes 33.87 seconds (2673.87 seconds total)