Starting phenix.real_space_refine on Fri Aug 2 22:02:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2024/7n62_24192_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 17 5.16 5 C 3569 2.51 5 N 933 2.21 5 O 1094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L GLU 165": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5613 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2235 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain: "H" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1689 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1619 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.69, per 1000 atoms: 0.66 Number of scatterers: 5613 At special positions: 0 Unit cell: (64.35, 95.7, 122.925, 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 17 16.00 O 1094 8.00 N 933 7.00 C 3569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1314 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 16 sheets defined 5.3% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.558A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 195 through 199 Processing helix chain 'L' and resid 29 through 32 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.775A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 182 through 188 removed outlier: 4.097A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 3.628A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.649A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.651A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.062A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.865A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 132 through 133 removed outlier: 4.376A pdb=" N LEU H 148 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 192 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 132 through 133 removed outlier: 4.376A pdb=" N LEU H 148 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 192 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER H 187 " --> pdb=" O VAL H 179 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.631A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.731A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS L 194 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 429 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: 1.57 Time building geometry restraints manager: 2.50 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: 1779 1.34 - 1.46: 1526 1.46 - 1.59: 2431 1.59 - 1.71: 0 1.71 - 1.83: 22 Bond restraints: 5758 Sorted by residual: bond pdb=" N GLU H 6 " pdb=" CA GLU H 6 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.33e+00 bond pdb=" N ASP A 253 " pdb=" CA ASP A 253 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.50e-02 4.44e+03 5.06e+00 bond pdb=" C ALA H 92 " pdb=" N VAL H 93 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.24e-02 6.50e+03 2.83e+00 bond pdb=" CB PRO H 159 " pdb=" CG PRO H 159 " ideal model delta sigma weight residual 1.506 1.567 -0.061 3.90e-02 6.57e+02 2.41e+00 bond pdb=" CB TRP H 36 " pdb=" CG TRP H 36 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.97e+00 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.47: 164 106.47 - 113.36: 3129 113.36 - 120.25: 1921 120.25 - 127.14: 2556 127.14 - 134.02: 62 Bond angle restraints: 7832 Sorted by residual: angle pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 120.60 113.12 7.48 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N TYR A 144 " pdb=" CA TYR A 144 " pdb=" C TYR A 144 " ideal model delta sigma weight residual 108.46 113.39 -4.93 1.51e+00 4.39e-01 1.07e+01 angle pdb=" CA PRO H 159 " pdb=" N PRO H 159 " pdb=" CD PRO H 159 " ideal model delta sigma weight residual 111.50 107.46 4.04 1.40e+00 5.10e-01 8.34e+00 angle pdb=" CA GLU A 96 " pdb=" CB GLU A 96 " pdb=" CG GLU A 96 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta sigma weight residual 127.00 133.63 -6.63 2.40e+00 1.74e-01 7.62e+00 ... (remaining 7827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3112 17.83 - 35.66: 280 35.66 - 53.49: 54 53.49 - 71.32: 8 71.32 - 89.14: 4 Dihedral angle restraints: 3458 sinusoidal: 1396 harmonic: 2062 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual 93.00 36.85 56.15 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta harmonic sigma weight residual 180.00 152.77 27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA PRO A 82 " pdb=" C PRO A 82 " pdb=" N VAL A 83 " pdb=" CA VAL A 83 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 839 0.106 - 0.213: 32 0.213 - 0.319: 2 0.319 - 0.425: 1 0.425 - 0.532: 1 Chirality restraints: 875 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.07e+00 chirality pdb=" CB ILE A 210 " pdb=" CA ILE A 210 " pdb=" CG1 ILE A 210 " pdb=" CG2 ILE A 210 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB ILE L 76 " pdb=" CA ILE L 76 " pdb=" CG1 ILE L 76 " pdb=" CG2 ILE L 76 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 872 not shown) Planarity restraints: 1005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 119 " -0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO L 120 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " -0.057 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO H 159 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 135 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO H 136 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 136 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 136 " -0.030 5.00e-02 4.00e+02 ... (remaining 1002 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 764 2.74 - 3.28: 6066 3.28 - 3.82: 9555 3.82 - 4.36: 11231 4.36 - 4.90: 18714 Nonbonded interactions: 46330 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" OH TYR A 160 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLN L 166 " pdb=" OG SER L 171 " model vdw 2.209 3.040 nonbonded pdb=" NH2 ARG A 158 " pdb=" OD1 ASP H 101 " model vdw 2.212 3.120 nonbonded pdb=" O GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.217 3.120 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.229 3.040 ... (remaining 46325 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.590 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: 0.040 Set scattering table: 0.060 Process input model: 19.750 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 : 0.006 0.061 5758 Z= 0.418 Angle : 0.825 8.203 7832 Z= 0.444 Chirality : 0.053 0.532 875 Planarity : 0.006 0.092 1000 Dihedral : 13.902 89.144 2126 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.74 (0.31), residues: 706 helix: -2.65 (1.15), residues: 14 sheet: -1.13 (0.31), residues: 269 loop : -2.35 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 258 HIS 0.003 0.001 HIS H 35 PHE 0.020 0.002 PHE L 72 TYR 0.035 0.002 TYR A 144 ARG 0.005 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.6470 (t) cc_final: 0.6260 (t) REVERT: A 56 LEU cc_start: 0.9064 (tp) cc_final: 0.8691 (tp) REVERT: A 100 ILE cc_start: 0.9421 (tt) cc_final: 0.9202 (tt) REVERT: H 90 ASP cc_start: 0.9094 (m-30) cc_final: 0.8846 (m-30) REVERT: H 99 ASP cc_start: 0.9256 (t0) cc_final: 0.8997 (t0) REVERT: H 104 TYR cc_start: 0.8107 (t80) cc_final: 0.7561 (t80) REVERT: L 88 TYR cc_start: 0.9417 (m-80) cc_final: 0.9138 (m-80) REVERT: L 139 PHE cc_start: 0.8581 (p90) cc_final: 0.8362 (p90) REVERT: L 142 ARG cc_start: 0.8410 (tpt90) cc_final: 0.8165 (tpt90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1603 time to fit residues: 26.6553 Evaluate side-chains 94 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 40 optimal weight: 40.0000 chunk 63 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5758 Z= 0.271 Angle : 0.773 9.241 7832 Z= 0.403 Chirality : 0.051 0.461 875 Planarity : 0.006 0.071 1000 Dihedral : 6.957 56.935 880 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.65 % Allowed : 12.48 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.60 (0.30), residues: 706 helix: -1.77 (1.17), residues: 14 sheet: -1.03 (0.29), residues: 273 loop : -2.30 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 258 HIS 0.008 0.001 HIS A 146 PHE 0.017 0.002 PHE L 72 TYR 0.022 0.002 TYR A 144 ARG 0.006 0.001 ARG L 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LEU cc_start: 0.9019 (tp) cc_final: 0.8612 (tp) REVERT: A 91 TYR cc_start: 0.9271 (t80) cc_final: 0.8880 (t80) REVERT: A 156 GLU cc_start: 0.8494 (pt0) cc_final: 0.8173 (pt0) REVERT: A 157 PHE cc_start: 0.8759 (m-80) cc_final: 0.8539 (m-10) REVERT: H 90 ASP cc_start: 0.8932 (m-30) cc_final: 0.8660 (m-30) REVERT: L 88 TYR cc_start: 0.9365 (m-80) cc_final: 0.9148 (m-80) REVERT: L 90 GLN cc_start: 0.8483 (tt0) cc_final: 0.8187 (tt0) REVERT: L 139 PHE cc_start: 0.8674 (p90) cc_final: 0.8359 (p90) REVERT: L 142 ARG cc_start: 0.8487 (tpt90) cc_final: 0.8137 (tpt90) outliers start: 4 outliers final: 3 residues processed: 119 average time/residue: 0.1634 time to fit residues: 25.6062 Evaluate side-chains 98 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5758 Z= 0.194 Angle : 0.719 8.185 7832 Z= 0.369 Chirality : 0.050 0.425 875 Planarity : 0.006 0.063 1000 Dihedral : 6.378 52.643 880 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 1.62 % Allowed : 15.72 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -2.36 (0.30), residues: 706 helix: -1.35 (1.24), residues: 14 sheet: -0.86 (0.28), residues: 296 loop : -2.19 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 258 HIS 0.003 0.001 HIS A 146 PHE 0.023 0.002 PHE L 209 TYR 0.016 0.001 TYR A 145 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 56 LEU cc_start: 0.8934 (tp) cc_final: 0.8514 (tp) REVERT: A 154 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 156 GLU cc_start: 0.8385 (pt0) cc_final: 0.8079 (pt0) REVERT: A 157 PHE cc_start: 0.8615 (m-80) cc_final: 0.8354 (m-10) REVERT: A 253 ASP cc_start: 0.7190 (m-30) cc_final: 0.6898 (m-30) REVERT: H 74 ASN cc_start: 0.8599 (m-40) cc_final: 0.7888 (m-40) REVERT: H 90 ASP cc_start: 0.8926 (m-30) cc_final: 0.8610 (m-30) REVERT: H 161 THR cc_start: 0.8914 (m) cc_final: 0.8638 (p) REVERT: L 88 TYR cc_start: 0.9356 (m-80) cc_final: 0.9113 (m-80) REVERT: L 90 GLN cc_start: 0.8471 (tt0) cc_final: 0.8234 (tt0) REVERT: L 139 PHE cc_start: 0.8609 (p90) cc_final: 0.8366 (p90) REVERT: L 140 TYR cc_start: 0.7873 (t80) cc_final: 0.7506 (t80) REVERT: L 142 ARG cc_start: 0.8440 (tpt90) cc_final: 0.8016 (tpt90) outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.1942 time to fit residues: 32.1626 Evaluate side-chains 107 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain H residue 145 THR Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2965 > 50: distance: 23 - 28: 29.028 distance: 28 - 29: 14.288 distance: 29 - 30: 14.949 distance: 29 - 32: 16.503 distance: 30 - 31: 17.221 distance: 30 - 35: 10.052 distance: 32 - 33: 23.052 distance: 32 - 34: 27.534 distance: 35 - 36: 14.311 distance: 35 - 195: 21.087 distance: 36 - 37: 33.601 distance: 36 - 39: 25.362 distance: 37 - 38: 35.305 distance: 37 - 43: 46.583 distance: 38 - 192: 21.132 distance: 39 - 40: 29.128 distance: 40 - 41: 37.350 distance: 40 - 42: 20.979 distance: 43 - 44: 20.022 distance: 43 - 49: 35.750 distance: 44 - 45: 20.231 distance: 44 - 47: 21.688 distance: 45 - 46: 18.732 distance: 45 - 50: 21.412 distance: 47 - 48: 18.388 distance: 48 - 49: 11.278 distance: 50 - 51: 20.859 distance: 51 - 52: 19.772 distance: 51 - 54: 7.193 distance: 52 - 53: 24.588 distance: 52 - 61: 23.813 distance: 54 - 55: 28.322 distance: 55 - 56: 29.538 distance: 55 - 57: 16.838 distance: 56 - 58: 23.413 distance: 57 - 59: 34.710 distance: 58 - 60: 14.078 distance: 59 - 60: 25.904 distance: 61 - 62: 5.606 distance: 62 - 63: 19.108 distance: 62 - 65: 9.535 distance: 63 - 64: 15.318 distance: 63 - 69: 23.384 distance: 65 - 66: 20.007 distance: 66 - 67: 9.565 distance: 66 - 68: 3.642 distance: 69 - 70: 11.595 distance: 70 - 71: 7.452 distance: 70 - 73: 17.126 distance: 71 - 72: 18.046 distance: 71 - 77: 25.381 distance: 73 - 74: 30.822 distance: 74 - 75: 35.529 distance: 74 - 76: 14.286 distance: 77 - 78: 24.757 distance: 78 - 79: 22.936 distance: 79 - 80: 31.715 distance: 79 - 81: 31.614 distance: 81 - 82: 27.895 distance: 81 - 158: 24.121 distance: 82 - 83: 8.621 distance: 82 - 85: 16.878 distance: 83 - 84: 20.381 distance: 83 - 88: 9.355 distance: 84 - 155: 27.468 distance: 85 - 86: 20.413 distance: 85 - 87: 4.066 distance: 88 - 89: 9.871 distance: 88 - 232: 17.912 distance: 89 - 90: 7.722 distance: 89 - 92: 14.941 distance: 90 - 91: 6.841 distance: 90 - 100: 5.254 distance: 91 - 229: 20.832 distance: 92 - 93: 9.420 distance: 95 - 97: 12.788 distance: 96 - 98: 8.073 distance: 97 - 98: 4.822 distance: 98 - 99: 8.796 distance: 100 - 101: 17.779 distance: 100 - 144: 18.477 distance: 101 - 102: 9.400 distance: 101 - 104: 11.147 distance: 102 - 103: 17.534 distance: 102 - 111: 9.948 distance: 103 - 141: 20.719 distance: 104 - 105: 10.902 distance: 105 - 106: 4.957 distance: 105 - 107: 9.474 distance: 106 - 108: 10.006 distance: 107 - 109: 9.460 distance: 108 - 110: 9.228 distance: 109 - 110: 9.948