Starting phenix.real_space_refine on Thu Nov 14 12:09:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/11_2024/7czb_30508.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/11_2024/7czb_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_30508/11_2024/7czb_30508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/11_2024/7czb_30508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/11_2024/7czb_30508.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7czb_30508/11_2024/7czb_30508.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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 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. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.29, per 1000 atoms: 0.68 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 - 3.00 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: 1.27 Conformation dependent library (CDL) restraints added in 1.0 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: 0.55 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: 1.53 Time building geometry restraints manager: 1.52 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: 0.00 - 2.41: 8550 2.41 - 4.83: 301 4.83 - 7.24: 47 7.24 - 9.66: 29 9.66 - 12.07: 1 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 3.120 nonbonded pdb=" O ILE A 159 " pdb=" ND2 ASN A 163 " model vdw 2.362 3.120 nonbonded pdb=" O TRP A 133 " pdb=" ND2 ASN A 137 " model vdw 2.375 3.120 nonbonded pdb=" O TRP C 133 " pdb=" ND2 ASN C 137 " model vdw 2.376 3.120 nonbonded pdb=" O TYR A 131 " pdb=" NE2 GLN A 135 " model vdw 2.383 3.120 ... (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 Time spend for trying shortcut: 0.00 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 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: 1.270 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.350 Find NCS groups from input model: 0.190 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 % Allowed : 11.01 % Favored : 88.52 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 145 HIS 0.001 0.000 HIS A 181 PHE 0.030 0.002 PHE B 188 TYR 0.016 0.002 TYR A 183 ARG 0.005 0.001 ARG B 138 *********************** 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 to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8599 (ttp) cc_final: 0.8369 (tmm) REVERT: A 183 TYR cc_start: 0.8821 (t80) cc_final: 0.8586 (t80) REVERT: B 59 THR cc_start: 0.9027 (p) cc_final: 0.8815 (m) REVERT: B 104 PHE cc_start: 0.8742 (t80) cc_final: 0.8368 (t80) REVERT: B 123 ILE cc_start: 0.8975 (mp) cc_final: 0.8457 (mm) REVERT: B 162 PHE cc_start: 0.7562 (m-10) cc_final: 0.7297 (m-80) REVERT: B 185 PHE cc_start: 0.8702 (t80) cc_final: 0.8494 (t80) REVERT: C 187 MET cc_start: 0.7799 (tmm) cc_final: 0.7245 (tmm) REVERT: D 85 ARG cc_start: 0.8550 (mmt90) cc_final: 0.8145 (mmm-85) REVERT: D 104 PHE cc_start: 0.8810 (t80) cc_final: 0.8351 (t80) REVERT: D 106 TRP cc_start: 0.8995 (t60) cc_final: 0.8347 (t60) REVERT: D 121 LEU cc_start: 0.9090 (tp) cc_final: 0.8878 (tp) REVERT: D 123 ILE cc_start: 0.9042 (mp) cc_final: 0.8460 (mm) outliers start: 3 outliers final: 0 residues processed: 234 average time/residue: 0.2049 time to fit residues: 61.7108 Evaluate side-chains 173 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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: 2.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 172 ASN B 177 ASN D 137 ASN D 172 ASN D 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6536 Z= 0.211 Angle : 0.776 8.970 8928 Z= 0.384 Chirality : 0.045 0.224 964 Planarity : 0.006 0.065 1084 Dihedral : 5.305 20.773 864 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.09 % Allowed : 20.60 % Favored : 75.31 % 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: -3.30 (0.29), residues: 768 helix: -1.05 (0.23), residues: 454 sheet: None (None), residues: 0 loop : -4.01 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.000 0.000 HIS D 181 PHE 0.013 0.001 PHE B 91 TYR 0.014 0.002 TYR B 77 ARG 0.006 0.001 ARG A 49 *********************** 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 223 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7387 (tmm) cc_final: 0.6987 (tmm) REVERT: B 104 PHE cc_start: 0.8762 (t80) cc_final: 0.8335 (t80) REVERT: B 106 TRP cc_start: 0.9008 (t60) cc_final: 0.8406 (t60) REVERT: B 136 LEU cc_start: 0.8747 (mm) cc_final: 0.8344 (mm) REVERT: C 187 MET cc_start: 0.7764 (tmm) cc_final: 0.7104 (tmm) REVERT: D 16 ARG cc_start: 0.7271 (ptt180) cc_final: 0.6994 (ptp-170) REVERT: D 85 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8114 (mmm-85) REVERT: D 104 PHE cc_start: 0.8789 (t80) cc_final: 0.8408 (t80) outliers start: 26 outliers final: 16 residues processed: 203 average time/residue: 0.1736 time to fit residues: 46.5409 Evaluate side-chains 192 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 23 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6536 Z= 0.222 Angle : 0.749 7.840 8928 Z= 0.366 Chirality : 0.045 0.208 964 Planarity : 0.005 0.066 1084 Dihedral : 5.004 20.476 864 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 5.50 % Allowed : 22.17 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.30), residues: 768 helix: -0.41 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -3.78 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 53 HIS 0.001 0.000 HIS D 181 PHE 0.018 0.001 PHE B 91 TYR 0.016 0.001 TYR B 98 ARG 0.004 0.001 ARG C 49 *********************** 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 224 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6248 (OUTLIER) cc_final: 0.5867 (m-10) REVERT: A 140 MET cc_start: 0.8063 (mpp) cc_final: 0.7861 (mpp) REVERT: A 183 TYR cc_start: 0.8822 (t80) cc_final: 0.8564 (t80) REVERT: A 187 MET cc_start: 0.7498 (tmm) cc_final: 0.6802 (tmm) REVERT: B 104 PHE cc_start: 0.8781 (t80) cc_final: 0.8344 (t80) REVERT: B 106 TRP cc_start: 0.9033 (t60) cc_final: 0.8450 (t60) REVERT: C 48 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5923 (m-10) REVERT: C 140 MET cc_start: 0.7728 (mpp) cc_final: 0.7409 (mpp) REVERT: C 187 MET cc_start: 0.7835 (tmm) cc_final: 0.7034 (tmm) REVERT: D 16 ARG cc_start: 0.7293 (ptt180) cc_final: 0.7009 (ptp-170) REVERT: D 85 ARG cc_start: 0.8633 (mmt90) cc_final: 0.8061 (tpp80) REVERT: D 104 PHE cc_start: 0.8816 (t80) cc_final: 0.8440 (t80) REVERT: D 118 MET cc_start: 0.6851 (tpp) cc_final: 0.6597 (tpt) outliers start: 35 outliers final: 19 residues processed: 202 average time/residue: 0.1620 time to fit residues: 43.2411 Evaluate side-chains 194 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: