Starting phenix.real_space_refine on Fri Sep 11 20:19:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r0c_4692/09_2026/6r0c_4692.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 284 5.49 5 S 10 5.16 5 C 6504 2.51 5 N 2186 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11737 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2887 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2935 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11737 At special positions: 0 Unit cell: (118.81, 77.39, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 10 16.00 P 284 15.00 O 2752 8.00 N 2186 7.00 C 6504 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 245.9 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 74.6% alpha, 1.9% beta 137 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.549A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.624A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.767A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.582A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.095A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.595A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.548A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.614A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.844A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.749A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.611A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.614A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.580A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.573A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.970A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.233A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.744A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.812A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.752A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.545A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.843A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.748A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.612A pdb=" N SER H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 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 96 through 97 removed outlier: 6.734A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.059A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.134A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 375 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1985 1.33 - 1.45: 4170 1.45 - 1.56: 5783 1.56 - 1.68: 566 1.68 - 1.80: 18 Bond restraints: 12522 Sorted by residual: bond pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " ideal model delta sigma weight residual 1.446 1.537 -0.091 1.00e-02 1.00e+04 8.27e+01 bond pdb=" C4' DC J -18 " pdb=" O4' DC J -18 " ideal model delta sigma weight residual 1.446 1.526 -0.080 1.00e-02 1.00e+04 6.47e+01 bond pdb=" C4' DC J -8 " pdb=" O4' DC J -8 " ideal model delta sigma weight residual 1.446 1.511 -0.065 1.00e-02 1.00e+04 4.24e+01 bond pdb=" C3' DT J 52 " pdb=" O3' DT J 52 " ideal model delta sigma weight residual 1.435 1.490 -0.055 1.30e-02 5.92e+03 1.76e+01 bond pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.61e+01 ... (remaining 12517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 16505 1.75 - 3.50: 1487 3.50 - 5.25: 117 5.25 - 7.00: 17 7.00 - 8.75: 5 Bond angle restraints: 18131 Sorted by residual: angle pdb=" O4' DT I 30 " pdb=" C1' DT I 30 " pdb=" N1 DT I 30 " ideal model delta sigma weight residual 108.00 112.71 -4.71 7.00e-01 2.04e+00 4.53e+01 angle pdb=" O5' DA I 57 " pdb=" C5' DA I 57 " pdb=" C4' DA I 57 " ideal model delta sigma weight residual 109.40 114.13 -4.73 8.00e-01 1.56e+00 3.50e+01 angle pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " pdb=" C1' DT J -19 " ideal model delta sigma weight residual 110.10 104.19 5.91 1.00e+00 1.00e+00 3.50e+01 angle pdb=" C4' DC J -18 " pdb=" O4' DC J -18 " pdb=" C1' DC J -18 " ideal model delta sigma weight residual 110.10 104.55 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " pdb=" P DG I 48 " ideal model delta sigma weight residual 119.70 126.04 -6.34 1.20e+00 6.94e-01 2.79e+01 ... (remaining 18126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5475 35.81 - 71.63: 1353 71.63 - 107.44: 12 107.44 - 143.25: 0 143.25 - 179.07: 6 Dihedral angle restraints: 6846 sinusoidal: 4687 harmonic: 2159 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN B 64 " pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1438 0.052 - 0.105: 531 0.105 - 0.157: 76 0.157 - 0.209: 12 0.209 - 0.262: 8 Chirality restraints: 2065 Sorted by residual: chirality pdb=" C4' DT J -19 " pdb=" C5' DT J -19 " pdb=" O4' DT J -19 " pdb=" C3' DT J -19 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C3' DG I 26 " pdb=" C4' DG I 26 " pdb=" O3' DG I 26 " pdb=" C2' DG I 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C4' DC J -8 " pdb=" C5' DC J -8 " pdb=" O4' DC J -8 " pdb=" C3' DC J -8 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2062 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C GLU B 63 " -0.067 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 60 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C VAL B 60 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL B 60 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE B 61 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 57 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL B 57 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 33 2.50 - 3.10: 7576 3.10 - 3.70: 19941 3.70 - 4.30: 28089 4.30 - 4.90: 40773 Nonbonded interactions: 96412 Sorted by model distance: nonbonded pdb=" O2 DC I 42 " pdb=" N2 DG J -42 " model vdw 1.900 2.496 nonbonded pdb=" O2 DC I 37 " pdb=" N2 DG J -37 " model vdw 2.083 2.496 nonbonded pdb=" N3 DC I 42 " pdb=" N1 DG J -42 " model vdw 2.204 2.560 nonbonded pdb=" N3 DC I 37 " pdb=" N1 DG J -37 " model vdw 2.251 2.560 nonbonded pdb=" N2 DG I -2 " pdb=" O2 DC J 2 " model vdw 2.275 2.496 ... (remaining 96407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } 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=1.00 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: 1.540 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 12522 Z= 0.678 Angle : 1.002 8.749 18131 Z= 0.827 Chirality : 0.054 0.262 2065 Planarity : 0.007 0.051 1312 Dihedral : 27.863 179.067 5456 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.26), residues: 731 helix: -1.06 (0.18), residues: 523 sheet: None (None), residues: 0 loop : -2.54 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.019 0.002 TYR F 51 PHE 0.026 0.002 PHE E 104 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.68 (12522) covalent geometry : angle 1.00231 / 0.83 (18131) hydrogen bonds : bond 0.16245 / 10.96 ( 709) hydrogen bonds : angle 5.12258 / 3.57 ( 1771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9551 (p) cc_final: 0.9257 (t) REVERT: A 93 GLN cc_start: 0.8725 (tt0) cc_final: 0.8077 (tt0) REVERT: A 94 GLU cc_start: 0.8173 (tp30) cc_final: 0.7781 (tp30) REVERT: A 97 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7911 (mt-10) REVERT: B 34 ILE cc_start: 0.9750 (mt) cc_final: 0.9543 (mm) REVERT: B 58 LEU cc_start: 0.9571 (tp) cc_final: 0.9181 (tt) REVERT: B 88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8391 (m-10) REVERT: C 84 GLN cc_start: 0.9271 (tp40) cc_final: 0.8896 (tp40) REVERT: C 111 ILE cc_start: 0.9037 (mm) cc_final: 0.8689 (tp) REVERT: E 58 THR cc_start: 0.9359 (p) cc_final: 0.9126 (t) REVERT: E 93 GLN cc_start: 0.8507 (tt0) cc_final: 0.8298 (tt0) REVERT: E 107 THR cc_start: 0.9633 (m) cc_final: 0.9370 (p) REVERT: F 43 VAL cc_start: 0.9509 (t) cc_final: 0.9282 (p) REVERT: F 88 TYR cc_start: 0.9076 (m-10) cc_final: 0.7956 (m-10) REVERT: G 84 GLN cc_start: 0.9249 (tp40) cc_final: 0.8926 (tp-100) REVERT: H 42 LEU cc_start: 0.9325 (tp) cc_final: 0.9089 (tp) REVERT: H 49 THR cc_start: 0.8357 (p) cc_final: 0.8061 (p) REVERT: H 79 HIS cc_start: 0.8519 (t70) cc_final: 0.8296 (t70) REVERT: H 80 TYR cc_start: 0.8270 (m-10) cc_final: 0.8042 (m-10) REVERT: H 90 GLU cc_start: 0.9123 (mp0) cc_final: 0.8908 (mp0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1514 time to fit residues: 61.4620 Evaluate side-chains 185 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN E 68 GLN E 85 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.085687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.057016 restraints weight = 40786.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058165 restraints weight = 24691.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.058917 restraints weight = 18508.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.059316 restraints weight = 15779.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.059463 restraints weight = 14525.085| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12522 Z= 0.168 Angle : 0.742 11.518 18131 Z= 0.430 Chirality : 0.052 0.302 2065 Planarity : 0.006 0.067 1312 Dihedral : 32.206 176.758 3991 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.30), residues: 731 helix: 0.76 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -2.29 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 45 TYR 0.014 0.002 TYR F 51 PHE 0.008 0.001 PHE A 78 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (12522) covalent geometry : angle 0.74232 / 0.43 (18131) hydrogen bonds : bond 0.08137 / 5.74 ( 709) hydrogen bonds : angle 3.25576 / 2.34 ( 1771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8930 (tt0) cc_final: 0.8430 (tt0) REVERT: A 94 GLU cc_start: 0.8406 (tp30) cc_final: 0.7979 (tp30) REVERT: A 97 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7793 (mt-10) REVERT: B 88 TYR cc_start: 0.8587 (m-10) cc_final: 0.8153 (m-10) REVERT: C 78 ILE cc_start: 0.8741 (mm) cc_final: 0.8451 (mm) REVERT: C 84 GLN cc_start: 0.9413 (tp40) cc_final: 0.8965 (tp40) REVERT: D 68 GLU cc_start: 0.8352 (tp30) cc_final: 0.8076 (tp30) REVERT: E 133 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7653 (mt-10) REVERT: F 43 VAL cc_start: 0.9417 (t) cc_final: 0.9066 (p) REVERT: F 88 TYR cc_start: 0.8706 (m-10) cc_final: 0.8092 (m-10) REVERT: G 39 TYR cc_start: 0.9027 (m-80) cc_final: 0.8808 (m-80) REVERT: G 84 GLN cc_start: 0.9335 (tp40) cc_final: 0.8157 (tm-30) REVERT: H 49 THR cc_start: 0.8414 (p) cc_final: 0.8190 (p) REVERT: H 64 ASN cc_start: 0.9156 (m-40) cc_final: 0.8746 (t0) REVERT: H 80 TYR cc_start: 0.7951 (m-10) cc_final: 0.7711 (m-10) REVERT: H 90 GLU cc_start: 0.9338 (mp0) cc_final: 0.8999 (mp0) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1212 time to fit residues: 40.7635 Evaluate side-chains 184 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN E 125 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.054392 restraints weight = 42060.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055614 restraints weight = 27474.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.056457 restraints weight = 18893.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.056460 restraints weight = 16830.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.056499 restraints weight = 16124.366| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12522 Z= 0.289 Angle : 0.817 16.100 18131 Z= 0.455 Chirality : 0.052 0.343 2065 Planarity : 0.005 0.044 1312 Dihedral : 32.012 177.270 3991 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.32 % Allowed : 4.21 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.30), residues: 731 helix: 1.32 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.35 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 71 TYR 0.018 0.002 TYR C 39 PHE 0.016 0.002 PHE G 25 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.29 (12522) covalent geometry : angle 0.81741 / 0.46 (18131) hydrogen bonds : bond 0.08358 / 5.83 ( 709) hydrogen bonds : angle 3.66047 / 2.59 ( 1771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9351 (mp) cc_final: 0.9144 (mp) REVERT: A 57 SER cc_start: 0.8921 (p) cc_final: 0.8716 (p) REVERT: A 60 LEU cc_start: 0.8710 (mm) cc_final: 0.8269 (mm) REVERT: A 93 GLN cc_start: 0.9146 (tt0) cc_final: 0.8843 (tt0) REVERT: A 94 GLU cc_start: 0.8460 (tp30) cc_final: 0.7894 (tp30) REVERT: A 97 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8230 (mt-10) REVERT: A 120 MET cc_start: 0.9157 (mtt) cc_final: 0.8834 (mtp) REVERT: A 133 GLU cc_start: 0.7717 (pp20) cc_final: 0.7240 (pp20) REVERT: B 53 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8188 (mp0) REVERT: B 88 TYR cc_start: 0.8675 (m-10) cc_final: 0.8382 (m-10) REVERT: B 93 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 78 ILE cc_start: 0.8601 (mm) cc_final: 0.8331 (mm) REVERT: C 84 GLN cc_start: 0.9467 (tp40) cc_final: 0.9137 (tp40) REVERT: D 44 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8475 (tm-30) REVERT: E 50 GLU cc_start: 0.9195 (mp0) cc_final: 0.8963 (mp0) REVERT: E 133 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7485 (mt-10) REVERT: F 43 VAL cc_start: 0.9518 (t) cc_final: 0.9230 (p) REVERT: F 45 ARG cc_start: 0.8696 (ttt180) cc_final: 0.8349 (ttm170) REVERT: G 56 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7969 (mm-30) REVERT: G 84 GLN cc_start: 0.9376 (tp40) cc_final: 0.9091 (tp-100) REVERT: H 31 LYS cc_start: 0.7997 (mmmm) cc_final: 0.7740 (mmmt) REVERT: H 64 ASN cc_start: 0.9179 (m-40) cc_final: 0.8800 (t0) REVERT: H 65 ASP cc_start: 0.8789 (t70) cc_final: 0.8574 (t0) REVERT: H 90 GLU cc_start: 0.9381 (mp0) cc_final: 0.9024 (mp0) outliers start: 2 outliers final: 2 residues processed: 210 average time/residue: 0.1292 time to fit residues: 36.7282 Evaluate side-chains 164 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 84 optimal weight: 50.0000 chunk 13 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 85 optimal weight: 40.0000 chunk 50 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.056448 restraints weight = 40858.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.057583 restraints weight = 25714.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.058276 restraints weight = 19567.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058722 restraints weight = 16883.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.058823 restraints weight = 15551.959| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12522 Z= 0.160 Angle : 0.689 13.616 18131 Z= 0.399 Chirality : 0.048 0.368 2065 Planarity : 0.004 0.034 1312 Dihedral : 31.910 177.789 3991 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.31), residues: 731 helix: 1.82 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.22 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.012 0.002 TYR E 41 PHE 0.018 0.002 PHE H 62 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (12522) covalent geometry : angle 0.68905 / 0.40 (18131) hydrogen bonds : bond 0.07042 / 4.93 ( 709) hydrogen bonds : angle 3.03935 / 2.16 ( 1771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9356 (mp) cc_final: 0.9122 (mp) REVERT: A 93 GLN cc_start: 0.9028 (tt0) cc_final: 0.8743 (tt0) REVERT: A 94 GLU cc_start: 0.8394 (tp30) cc_final: 0.7991 (tp30) REVERT: A 120 MET cc_start: 0.9062 (mtt) cc_final: 0.8790 (mtp) REVERT: A 133 GLU cc_start: 0.7467 (pp20) cc_final: 0.7132 (pp20) REVERT: B 88 TYR cc_start: 0.8719 (m-10) cc_final: 0.8440 (m-10) REVERT: B 93 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8217 (tm-30) REVERT: C 84 GLN cc_start: 0.9456 (tp40) cc_final: 0.9085 (tp40) REVERT: C 100 VAL cc_start: 0.9518 (t) cc_final: 0.9209 (p) REVERT: D 44 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8503 (tm-30) REVERT: D 56 MET cc_start: 0.9018 (tpp) cc_final: 0.8813 (tpp) REVERT: E 133 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7457 (mt-10) REVERT: F 43 VAL cc_start: 0.9439 (t) cc_final: 0.9149 (p) REVERT: F 45 ARG cc_start: 0.8620 (ttt180) cc_final: 0.8368 (ttm170) REVERT: G 64 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8213 (tm-30) REVERT: G 84 GLN cc_start: 0.9358 (tp40) cc_final: 0.8776 (tm-30) REVERT: H 64 ASN cc_start: 0.9123 (m-40) cc_final: 0.8805 (t0) REVERT: H 65 ASP cc_start: 0.8789 (t70) cc_final: 0.8531 (t0) REVERT: H 76 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8788 (ttm110) REVERT: H 90 GLU cc_start: 0.9323 (mp0) cc_final: 0.8923 (mp0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1224 time to fit residues: 36.9383 Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.085581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.057122 restraints weight = 41559.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.058441 restraints weight = 26509.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059220 restraints weight = 18221.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.059231 restraints weight = 16503.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059324 restraints weight = 15839.689| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12522 Z= 0.143 Angle : 0.668 13.229 18131 Z= 0.386 Chirality : 0.047 0.355 2065 Planarity : 0.004 0.034 1312 Dihedral : 31.779 177.072 3991 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.31), residues: 731 helix: 2.09 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.07 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 83 TYR 0.015 0.001 TYR E 41 PHE 0.009 0.001 PHE F 61 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.14 (12522) covalent geometry : angle 0.66770 / 0.39 (18131) hydrogen bonds : bond 0.06558 / 4.61 ( 709) hydrogen bonds : angle 2.85714 / 2.03 ( 1771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9360 (mp) cc_final: 0.9151 (mp) REVERT: A 93 GLN cc_start: 0.8923 (tt0) cc_final: 0.8056 (tt0) REVERT: A 94 GLU cc_start: 0.8283 (tp30) cc_final: 0.7931 (tp30) REVERT: A 97 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 88 TYR cc_start: 0.8689 (m-10) cc_final: 0.8438 (m-10) REVERT: C 84 GLN cc_start: 0.9445 (tp40) cc_final: 0.9019 (tp40) REVERT: C 100 VAL cc_start: 0.9522 (t) cc_final: 0.9237 (p) REVERT: D 44 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8538 (tm-30) REVERT: E 61 LEU cc_start: 0.9372 (mt) cc_final: 0.9022 (mt) REVERT: E 133 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7564 (mt-10) REVERT: F 43 VAL cc_start: 0.9454 (t) cc_final: 0.9139 (p) REVERT: F 45 ARG cc_start: 0.8565 (ttt180) cc_final: 0.8327 (ttm170) REVERT: F 59 LYS cc_start: 0.9140 (tttm) cc_final: 0.8696 (ttpt) REVERT: F 84 MET cc_start: 0.8535 (mmt) cc_final: 0.8157 (mmm) REVERT: G 39 TYR cc_start: 0.9049 (m-80) cc_final: 0.8779 (m-80) REVERT: G 84 GLN cc_start: 0.9298 (tp40) cc_final: 0.8277 (tm-30) REVERT: H 64 ASN cc_start: 0.9107 (m-40) cc_final: 0.8821 (t0) REVERT: H 65 ASP cc_start: 0.8719 (t70) cc_final: 0.8470 (t0) REVERT: H 90 GLU cc_start: 0.9335 (mp0) cc_final: 0.8926 (mp0) REVERT: H 102 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7218 (tm-30) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1157 time to fit residues: 37.4414 Evaluate side-chains 184 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 83 optimal weight: 40.0000 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 71 optimal weight: 50.0000 chunk 37 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.085499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.056769 restraints weight = 41642.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.057908 restraints weight = 25626.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058643 restraints weight = 19333.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059091 restraints weight = 16546.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.059305 restraints weight = 15219.928| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12522 Z= 0.166 Angle : 0.682 13.093 18131 Z= 0.390 Chirality : 0.047 0.295 2065 Planarity : 0.004 0.037 1312 Dihedral : 31.716 177.318 3991 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.31), residues: 731 helix: 2.14 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.93 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 42 TYR 0.008 0.001 TYR G 50 PHE 0.009 0.001 PHE F 61 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (12522) covalent geometry : angle 0.68158 / 0.39 (18131) hydrogen bonds : bond 0.06593 / 4.63 ( 709) hydrogen bonds : angle 2.97617 / 2.11 ( 1771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9407 (mp) cc_final: 0.9172 (mp) REVERT: A 93 GLN cc_start: 0.8953 (tt0) cc_final: 0.8111 (tt0) REVERT: A 94 GLU cc_start: 0.8302 (tp30) cc_final: 0.7914 (tp30) REVERT: A 97 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 120 MET cc_start: 0.8978 (mtt) cc_final: 0.8744 (mtp) REVERT: A 133 GLU cc_start: 0.8412 (pm20) cc_final: 0.7803 (pp20) REVERT: B 88 TYR cc_start: 0.8679 (m-10) cc_final: 0.8420 (m-10) REVERT: C 38 ASN cc_start: 0.9265 (m-40) cc_final: 0.9063 (m-40) REVERT: C 78 ILE cc_start: 0.8377 (mm) cc_final: 0.8111 (mm) REVERT: C 84 GLN cc_start: 0.9451 (tp40) cc_final: 0.9024 (tp40) REVERT: C 100 VAL cc_start: 0.9567 (t) cc_final: 0.9294 (p) REVERT: D 44 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8607 (tm-30) REVERT: D 56 MET cc_start: 0.9078 (tpp) cc_final: 0.8857 (tpp) REVERT: E 61 LEU cc_start: 0.9348 (mt) cc_final: 0.8901 (mt) REVERT: F 43 VAL cc_start: 0.9485 (t) cc_final: 0.9169 (p) REVERT: F 45 ARG cc_start: 0.8592 (ttt180) cc_final: 0.8286 (ttm170) REVERT: F 59 LYS cc_start: 0.9116 (tttm) cc_final: 0.8553 (tttt) REVERT: G 84 GLN cc_start: 0.9363 (tp-100) cc_final: 0.8800 (tm-30) REVERT: H 51 ILE cc_start: 0.9565 (mp) cc_final: 0.9329 (mm) REVERT: H 64 ASN cc_start: 0.9126 (m-40) cc_final: 0.8843 (t0) REVERT: H 65 ASP cc_start: 0.8731 (t70) cc_final: 0.8470 (t0) REVERT: H 90 GLU cc_start: 0.9341 (mp0) cc_final: 0.8947 (mp0) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1125 time to fit residues: 34.1316 Evaluate side-chains 177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 68 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.086714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.058352 restraints weight = 40907.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059512 restraints weight = 25218.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060265 restraints weight = 18979.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060685 restraints weight = 16193.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060685 restraints weight = 14929.811| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12522 Z= 0.143 Angle : 0.666 11.713 18131 Z= 0.384 Chirality : 0.046 0.291 2065 Planarity : 0.004 0.081 1312 Dihedral : 31.657 177.138 3991 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.31), residues: 731 helix: 2.13 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.76 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 39 TYR 0.017 0.001 TYR F 51 PHE 0.023 0.001 PHE A 104 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (12522) covalent geometry : angle 0.66618 / 0.38 (18131) hydrogen bonds : bond 0.06219 / 4.37 ( 709) hydrogen bonds : angle 2.79964 / 1.99 ( 1771) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9397 (mp) cc_final: 0.9179 (mp) REVERT: A 93 GLN cc_start: 0.8901 (tt0) cc_final: 0.8070 (tt0) REVERT: A 94 GLU cc_start: 0.8238 (tp30) cc_final: 0.7830 (tp30) REVERT: A 120 MET cc_start: 0.8900 (mtt) cc_final: 0.8651 (mtp) REVERT: C 38 ASN cc_start: 0.9218 (m-40) cc_final: 0.9010 (m-40) REVERT: C 78 ILE cc_start: 0.8384 (mm) cc_final: 0.8082 (mm) REVERT: C 84 GLN cc_start: 0.9403 (tp40) cc_final: 0.8993 (tp40) REVERT: C 100 VAL cc_start: 0.9551 (t) cc_final: 0.9227 (p) REVERT: D 44 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8649 (tm-30) REVERT: D 56 MET cc_start: 0.9031 (tpp) cc_final: 0.8801 (tpp) REVERT: F 43 VAL cc_start: 0.9521 (t) cc_final: 0.9156 (p) REVERT: F 84 MET cc_start: 0.8554 (mmt) cc_final: 0.8339 (mmt) REVERT: G 84 GLN cc_start: 0.9282 (tp-100) cc_final: 0.9036 (tm-30) REVERT: H 51 ILE cc_start: 0.9563 (mp) cc_final: 0.9357 (mm) REVERT: H 65 ASP cc_start: 0.8622 (t70) cc_final: 0.8366 (t0) REVERT: H 90 GLU cc_start: 0.9270 (mp0) cc_final: 0.8923 (mp0) REVERT: H 99 LEU cc_start: 0.9033 (mp) cc_final: 0.8800 (mp) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1116 time to fit residues: 34.7161 Evaluate side-chains 176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.086509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.057542 restraints weight = 41027.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.058607 restraints weight = 25550.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.059332 restraints weight = 19734.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.059798 restraints weight = 16813.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.059975 restraints weight = 15407.142| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12522 Z= 0.143 Angle : 0.659 11.128 18131 Z= 0.379 Chirality : 0.045 0.288 2065 Planarity : 0.004 0.039 1312 Dihedral : 31.610 176.261 3991 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.31), residues: 731 helix: 2.29 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.68 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 42 TYR 0.016 0.001 TYR B 88 PHE 0.009 0.001 PHE E 78 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12522) covalent geometry : angle 0.65948 / 0.38 (18131) hydrogen bonds : bond 0.06124 / 4.30 ( 709) hydrogen bonds : angle 2.84476 / 1.99 ( 1771) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9387 (mp) cc_final: 0.9151 (mp) REVERT: A 93 GLN cc_start: 0.8952 (tt0) cc_final: 0.8638 (tt0) REVERT: A 94 GLU cc_start: 0.8247 (tp30) cc_final: 0.7808 (tp30) REVERT: A 120 MET cc_start: 0.8883 (mtt) cc_final: 0.8649 (mtp) REVERT: A 133 GLU cc_start: 0.8436 (pm20) cc_final: 0.7851 (pp20) REVERT: C 84 GLN cc_start: 0.9438 (tp40) cc_final: 0.8995 (tp40) REVERT: C 110 ASN cc_start: 0.8750 (t0) cc_final: 0.8313 (p0) REVERT: D 44 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8671 (tm-30) REVERT: E 60 LEU cc_start: 0.9142 (mm) cc_final: 0.8940 (mm) REVERT: F 43 VAL cc_start: 0.9502 (t) cc_final: 0.9189 (p) REVERT: F 84 MET cc_start: 0.8615 (mmt) cc_final: 0.8260 (mmt) REVERT: G 84 GLN cc_start: 0.9283 (tp-100) cc_final: 0.9034 (tm-30) REVERT: H 65 ASP cc_start: 0.8705 (t70) cc_final: 0.8440 (t0) REVERT: H 90 GLU cc_start: 0.9274 (mp0) cc_final: 0.8915 (mp0) REVERT: H 99 LEU cc_start: 0.8973 (mp) cc_final: 0.8772 (mp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1195 time to fit residues: 36.3089 Evaluate side-chains 168 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 40.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.085867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.056777 restraints weight = 41824.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.058021 restraints weight = 27074.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.058677 restraints weight = 18815.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.058738 restraints weight = 17484.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.058807 restraints weight = 16684.131| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12522 Z= 0.185 Angle : 0.687 8.458 18131 Z= 0.395 Chirality : 0.046 0.309 2065 Planarity : 0.004 0.057 1312 Dihedral : 31.598 176.868 3991 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.31), residues: 731 helix: 2.18 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.80 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 29 TYR 0.012 0.002 TYR H 80 PHE 0.005 0.001 PHE E 104 HIS 0.010 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.19 (12522) covalent geometry : angle 0.68741 / 0.39 (18131) hydrogen bonds : bond 0.06389 / 4.46 ( 709) hydrogen bonds : angle 3.07367 / 2.15 ( 1771) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9380 (mp) cc_final: 0.9142 (mp) REVERT: A 93 GLN cc_start: 0.8906 (tt0) cc_final: 0.8115 (tt0) REVERT: A 94 GLU cc_start: 0.8253 (tp30) cc_final: 0.7830 (tp30) REVERT: A 97 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7928 (mt-10) REVERT: C 38 ASN cc_start: 0.9287 (m-40) cc_final: 0.9076 (m-40) REVERT: C 78 ILE cc_start: 0.8359 (mm) cc_final: 0.8135 (mm) REVERT: C 84 GLN cc_start: 0.9439 (tp40) cc_final: 0.9025 (tp40) REVERT: C 110 ASN cc_start: 0.8718 (t0) cc_final: 0.8311 (p0) REVERT: D 44 GLN cc_start: 0.8935 (tm-30) cc_final: 0.8688 (tm-30) REVERT: E 46 VAL cc_start: 0.8253 (p) cc_final: 0.7973 (p) REVERT: F 43 VAL cc_start: 0.9551 (t) cc_final: 0.9228 (p) REVERT: F 84 MET cc_start: 0.8694 (mmt) cc_final: 0.8369 (mmt) REVERT: G 84 GLN cc_start: 0.9303 (tp-100) cc_final: 0.8642 (tm-30) REVERT: H 65 ASP cc_start: 0.8768 (t70) cc_final: 0.8527 (t0) REVERT: H 90 GLU cc_start: 0.9306 (mp0) cc_final: 0.8931 (mp0) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1196 time to fit residues: 34.1160 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 88 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.058366 restraints weight = 40999.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.059490 restraints weight = 25422.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.060230 restraints weight = 19340.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.060645 restraints weight = 16617.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.060883 restraints weight = 15328.989| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12522 Z= 0.147 Angle : 0.665 8.342 18131 Z= 0.385 Chirality : 0.044 0.288 2065 Planarity : 0.004 0.032 1312 Dihedral : 31.552 177.275 3991 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.16 % Allowed : 0.16 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.31), residues: 731 helix: 2.17 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.72 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.016 0.001 TYR H 80 PHE 0.007 0.001 PHE A 104 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.15 (12522) covalent geometry : angle 0.66458 / 0.38 (18131) hydrogen bonds : bond 0.06094 / 4.26 ( 709) hydrogen bonds : angle 2.91224 / 2.03 ( 1771) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9388 (mp) cc_final: 0.9121 (mt) REVERT: A 93 GLN cc_start: 0.8851 (tt0) cc_final: 0.7993 (tt0) REVERT: A 97 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7929 (mt-10) REVERT: C 74 LYS cc_start: 0.9346 (tmtt) cc_final: 0.8978 (mmmt) REVERT: C 78 ILE cc_start: 0.8423 (mm) cc_final: 0.8208 (mm) REVERT: C 84 GLN cc_start: 0.9405 (tp40) cc_final: 0.9001 (tp40) REVERT: C 110 ASN cc_start: 0.8683 (t0) cc_final: 0.8328 (p0) REVERT: D 44 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8685 (tm-30) REVERT: F 43 VAL cc_start: 0.9549 (t) cc_final: 0.9260 (p) REVERT: F 84 MET cc_start: 0.8395 (mmt) cc_final: 0.8182 (mmt) REVERT: G 84 GLN cc_start: 0.9285 (tp-100) cc_final: 0.9067 (tm-30) REVERT: H 65 ASP cc_start: 0.8702 (t70) cc_final: 0.8446 (t0) REVERT: H 90 GLU cc_start: 0.9267 (mp0) cc_final: 0.8887 (mp0) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.1242 time to fit residues: 36.3330 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.085589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.056184 restraints weight = 41828.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.057247 restraints weight = 26396.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.057956 restraints weight = 20208.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.058339 restraints weight = 17446.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.058588 restraints weight = 16192.304| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12522 Z= 0.196 Angle : 0.693 8.340 18131 Z= 0.397 Chirality : 0.045 0.285 2065 Planarity : 0.004 0.035 1312 Dihedral : 31.537 177.605 3991 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.31), residues: 731 helix: 2.15 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.011 0.001 TYR C 39 PHE 0.017 0.001 PHE A 104 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (12522) covalent geometry : angle 0.69334 / 0.40 (18131) hydrogen bonds : bond 0.06526 / 4.54 ( 709) hydrogen bonds : angle 3.19271 / 2.23 ( 1771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.18 seconds wall clock time: 30 minutes 37.54 seconds (1837.54 seconds total)