Starting phenix.real_space_refine (version: dev) on Mon Apr 4 14:12:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/04_2022/7czb_30508.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.055 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 6304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 3.98, per 1000 atoms: 0.63 Number of scatterers: 6304 At special positions: 0 Unit cell: (116.1, 124.7, 70.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 988 8.00 N 968 7.00 C 4308 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: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 64.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Proline residue: A 26 - end of helix removed outlier: 3.569A pdb=" N GLY A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.924A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.556A pdb=" N LEU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.611A pdb=" N ASN A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.485A pdb=" N ILE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 136 removed outlier: 3.549A pdb=" N ILE A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.683A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 Proline residue: B 26 - end of helix removed outlier: 3.512A pdb=" N LEU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.452A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 70 through 90 removed outlier: 3.833A pdb=" N THR B 84 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 116 removed outlier: 4.277A pdb=" N TYR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 105 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.779A pdb=" N ILE B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 173 through 189 removed outlier: 3.895A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 32 Proline residue: C 26 - end of helix removed outlier: 3.578A pdb=" N GLY C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.948A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 89 removed outlier: 3.550A pdb=" N LEU C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR C 84 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.561A pdb=" N TYR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 105 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 116 removed outlier: 4.540A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 136 removed outlier: 3.548A pdb=" N ILE C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 166 Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.663A pdb=" N LEU C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 Proline residue: D 26 - end of helix removed outlier: 3.555A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.442A pdb=" N TYR D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 70 through 90 removed outlier: 3.890A pdb=" N THR D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 116 removed outlier: 4.255A pdb=" N TYR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 105 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.772A pdb=" N ILE D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 173 through 189 removed outlier: 3.880A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1692 1.34 - 1.46: 1757 1.46 - 1.58: 3013 1.58 - 1.70: 2 1.70 - 1.82: 72 Bond restraints: 6536 Sorted by residual: bond pdb=" CA THR C 68 " pdb=" CB THR C 68 " ideal model delta sigma weight residual 1.526 1.566 -0.040 1.51e-02 4.39e+03 6.88e+00 bond pdb=" C ILE B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.80e+00 bond pdb=" C ILE D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.69e+00 bond pdb=" CB ASP C 139 " pdb=" CG ASP C 139 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.05e+00 ... (remaining 6531 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 206 106.17 - 113.13: 3148 113.13 - 120.10: 2681 120.10 - 127.06: 2762 127.06 - 134.02: 131 Bond angle restraints: 8928 Sorted by residual: angle pdb=" C ARG C 138 " pdb=" N ASP C 139 " pdb=" CA ASP C 139 " ideal model delta sigma weight residual 121.54 133.61 -12.07 1.91e+00 2.74e-01 4.00e+01 angle pdb=" C ALA C 24 " pdb=" N VAL C 25 " pdb=" CA VAL C 25 " ideal model delta sigma weight residual 120.24 123.63 -3.39 6.30e-01 2.52e+00 2.89e+01 angle pdb=" C ALA A 24 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 120.24 123.49 -3.25 6.30e-01 2.52e+00 2.66e+01 angle pdb=" C ARG A 138 " pdb=" N ASP A 139 " pdb=" CA ASP A 139 " ideal model delta sigma weight residual 125.02 134.02 -9.00 1.76e+00 3.23e-01 2.61e+01 angle pdb=" C ALA D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 3073 15.62 - 31.23: 422 31.23 - 46.85: 115 46.85 - 62.46: 15 62.46 - 78.08: 11 Dihedral angle restraints: 3636 sinusoidal: 1384 harmonic: 2252 Sorted by residual: dihedral pdb=" CA ARG A 54 " pdb=" C ARG A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ARG C 54 " pdb=" C ARG C 54 " pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET D 118 " pdb=" C MET D 118 " pdb=" N GLN D 119 " pdb=" CA GLN D 119 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 837 0.091 - 0.183: 116 0.183 - 0.274: 9 0.274 - 0.365: 0 0.365 - 0.456: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" CB ILE C 11 " pdb=" CA ILE C 11 " pdb=" CG1 ILE C 11 " pdb=" CG2 ILE C 11 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA ARG C 94 " pdb=" N ARG C 94 " pdb=" C ARG C 94 " pdb=" CB ARG C 94 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 961 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 54 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO C 55 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 54 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 55 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 25 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 26 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.030 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2187 2.87 - 3.38: 5885 3.38 - 3.88: 9807 3.88 - 4.39: 9919 4.39 - 4.90: 17266 Nonbonded interactions: 45064 Sorted by model distance: nonbonded pdb=" O ILE C 159 " pdb=" ND2 ASN C 163 " model vdw 2.360 2.520 nonbonded pdb=" O ILE A 159 " pdb=" ND2 ASN A 163 " model vdw 2.362 2.520 nonbonded pdb=" O TRP A 133 " pdb=" ND2 ASN A 137 " model vdw 2.375 2.520 nonbonded pdb=" O TRP C 133 " pdb=" ND2 ASN C 137 " model vdw 2.376 2.520 nonbonded pdb=" O TYR A 131 " pdb=" NE2 GLN A 135 " model vdw 2.383 2.520 ... (remaining 45059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4308 2.51 5 N 968 2.21 5 O 988 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.760 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: 3.900 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 20.540 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.005 0.058 6536 Z= 0.314 Angle : 1.117 12.073 8928 Z= 0.601 Chirality : 0.063 0.456 964 Planarity : 0.007 0.082 1084 Dihedral : 15.722 78.075 2212 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.24), residues: 768 helix: -2.64 (0.18), residues: 430 sheet: None (None), residues: 0 loop : -4.19 (0.30), residues: 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 234 average time/residue: 0.1907 time to fit residues: 57.6501 Evaluate side-chains 177 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.0020 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 75 ASN B 81 GLN B 137 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN D 75 ASN D 137 ASN D 172 ASN D 177 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6536 Z= 0.195 Angle : 0.771 8.175 8928 Z= 0.379 Chirality : 0.045 0.224 964 Planarity : 0.005 0.067 1084 Dihedral : 5.304 21.123 864 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer Outliers : 4.72 % 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: -3.42 (0.29), residues: 768 helix: -1.16 (0.23), residues: 452 sheet: None (None), residues: 0 loop : -4.02 (0.33), residues: 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 205 average time/residue: 0.1561 time to fit residues: 42.7669 Evaluate side-chains 198 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 0.729 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0644 time to fit residues: 3.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 0.0770 chunk 19 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6536 Z= 0.201 Angle : 0.738 7.594 8928 Z= 0.358 Chirality : 0.044 0.207 964 Planarity : 0.005 0.063 1084 Dihedral : 4.943 19.922 864 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer Outliers : 4.09 % 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: -2.57 (0.30), residues: 768 helix: -0.41 (0.24), residues: 454 sheet: None (None), residues: 0 loop : -3.79 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 0.804 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 197 average time/residue: 0.1554 time to fit residues: 40.9382 Evaluate side-chains 189 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0578 time to fit residues: 2.4550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.0030 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 19 optimal weight: 10.0000 overall best weight: 0.4928 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 6536 Z= 0.172 Angle : 0.746 9.721 8928 Z= 0.354 Chirality : 0.044 0.204 964 Planarity : 0.004 0.059 1084 Dihedral : 4.744 18.752 864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.31), residues: 768 helix: -0.04 (0.25), residues: 452 sheet: None (None), residues: 0 loop : -3.69 (0.34), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 0.763 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.1488 time to fit residues: 43.4734 Evaluate side-chains 206 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 0.815 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0557 time to fit residues: 2.6252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.0980 chunk 30 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 65 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6536 Z= 0.174 Angle : 0.745 9.514 8928 Z= 0.348 Chirality : 0.044 0.201 964 Planarity : 0.004 0.029 1084 Dihedral : 4.575 17.654 864 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer Outliers : 1.26 % 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: -1.93 (0.31), residues: 768 helix: 0.16 (0.25), residues: 454 sheet: None (None), residues: 0 loop : -3.62 (0.34), residues: 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 213 average time/residue: 0.1604 time to fit residues: 45.4998 Evaluate side-chains 196 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0578 time to fit residues: 1.4875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.8003 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6536 Z= 0.186 Angle : 0.771 11.176 8928 Z= 0.357 Chirality : 0.044 0.200 964 Planarity : 0.004 0.043 1084 Dihedral : 4.502 16.658 864 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer Outliers : 3.14 % 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: -1.74 (0.32), residues: 768 helix: 0.31 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 198 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 206 average time/residue: 0.1553 time to fit residues: 43.0914 Evaluate side-chains 203 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0612 time to fit residues: 2.4434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 61 optimal weight: 0.0870 chunk 73 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 overall best weight: 0.4374 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 6536 Z= 0.183 Angle : 0.781 11.803 8928 Z= 0.360 Chirality : 0.045 0.198 964 Planarity : 0.004 0.043 1084 Dihedral : 4.435 16.290 864 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer Outliers : 2.20 % 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: -1.65 (0.32), residues: 768 helix: 0.39 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.54 (0.35), residues: 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 210 average time/residue: 0.1585 time to fit residues: 44.9991 Evaluate side-chains 195 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0655 time to fit residues: 2.0650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6536 Z= 0.197 Angle : 0.797 13.012 8928 Z= 0.369 Chirality : 0.045 0.198 964 Planarity : 0.004 0.051 1084 Dihedral : 4.428 16.015 864 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer Outliers : 1.73 % 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: -1.60 (0.32), residues: 768 helix: 0.43 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.52 (0.36), residues: 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 198 average time/residue: 0.1545 time to fit residues: 41.2582 Evaluate side-chains 193 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0645 time to fit residues: 1.6055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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: 0.7988 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6536 Z= 0.194 Angle : 0.821 13.709 8928 Z= 0.377 Chirality : 0.045 0.198 964 Planarity : 0.004 0.049 1084 Dihedral : 4.419 17.620 864 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.58 (0.32), residues: 768 helix: 0.44 (0.25), residues: 458 sheet: None (None), residues: 0 loop : -3.50 (0.36), residues: 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 195 average time/residue: 0.1533 time to fit residues: 40.2915 Evaluate side-chains 187 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0664 time to fit residues: 1.2437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 0.0040 chunk 16 optimal weight: 0.0070 overall best weight: 0.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6536 Z= 0.191 Angle : 0.839 14.402 8928 Z= 0.385 Chirality : 0.045 0.198 964 Planarity : 0.005 0.055 1084 Dihedral : 4.399 19.932 864 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 0.94 % 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: -1.61 (0.32), residues: 768 helix: 0.42 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.50 (0.35), residues: 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 202 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 203 average time/residue: 0.1524 time to fit residues: 41.8071 Evaluate side-chains 190 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 186 time to evaluate : 0.756 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0647 time to fit residues: 1.4337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN C 75 ASN C 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.147851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122441 restraints weight = 14542.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125355 restraints weight = 8717.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127356 restraints weight = 6356.833| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6536 Z= 0.205 Angle : 0.870 15.359 8928 Z= 0.402 Chirality : 0.046 0.198 964 Planarity : 0.005 0.061 1084 Dihedral : 4.478 23.433 864 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer Outliers : 0.63 % 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: -1.60 (0.32), residues: 768 helix: 0.38 (0.25), residues: 458 sheet: None (None), residues: 0 loop : -3.45 (0.36), residues: 310 =============================================================================== Job complete usr+sys time: 1543.92 seconds wall clock time: 28 minutes 29.30 seconds (1709.30 seconds total)