Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 20:57:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2023/7n62_24192_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2023/7n62_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_2023/7n62_24192.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2023/7n62_24192.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2023/7n62_24192_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n62_24192/08_2023/7n62_24192_neut.pdb" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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 chiralities: 5 Time building chain proxies: 3.39, per 1000 atoms: 0.60 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: 2.10 Conformation dependent library (CDL) restraints added in 797.9 milliseconds 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: 0.63 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: 1.76 Time building geometry restraints manager: 2.31 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: 3019 17.83 - 35.66: 274 35.66 - 53.49: 48 53.49 - 71.32: 8 71.32 - 89.14: 4 Dihedral angle restraints: 3353 sinusoidal: 1291 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 3350 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 2.440 nonbonded pdb=" OE1 GLN L 166 " pdb=" OG SER L 171 " model vdw 2.209 2.440 nonbonded pdb=" NH2 ARG A 158 " pdb=" OD1 ASP H 101 " model vdw 2.212 2.520 nonbonded pdb=" O GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.217 2.520 nonbonded pdb=" O TYR L 186 " pdb=" OH TYR L 192 " model vdw 2.229 2.440 ... (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 ========== 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: 0.720 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: 2.960 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.160 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- 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 : 13.984 89.144 2021 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 % 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 *********************** 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 : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1667 time to fit residues: 27.6884 Evaluate side-chains 91 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8550 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN L 39 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 5758 Z= 0.270 Angle : 0.747 8.856 7832 Z= 0.388 Chirality : 0.050 0.451 875 Planarity : 0.006 0.071 1000 Dihedral : 6.270 25.727 775 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer Outliers : 1.13 % 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: -2.58 (0.30), residues: 706 helix: -2.03 (1.13), residues: 14 sheet: -1.02 (0.29), residues: 276 loop : -2.27 (0.29), residues: 416 *********************** 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: 7 poor density : 113 time to evaluate : 0.680 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 117 average time/residue: 0.1797 time to fit residues: 27.5996 Evaluate side-chains 96 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0567 time to fit residues: 1.2645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 5758 Z= 0.247 Angle : 0.725 8.512 7832 Z= 0.370 Chirality : 0.049 0.421 875 Planarity : 0.005 0.066 1000 Dihedral : 6.057 26.251 775 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer Outliers : 1.62 % 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: -2.39 (0.30), residues: 706 helix: -1.65 (1.11), residues: 14 sheet: -0.98 (0.29), residues: 279 loop : -2.08 (0.30), residues: 413 *********************** 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 116 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 0.1689 time to fit residues: 25.2031 Evaluate side-chains 104 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0592 time to fit residues: 1.6822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 0.0570 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 5758 Z= 0.364 Angle : 0.750 8.507 7832 Z= 0.385 Chirality : 0.049 0.416 875 Planarity : 0.006 0.067 1000 Dihedral : 6.197 26.686 775 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer Outliers : 2.43 % 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: -2.41 (0.30), residues: 706 helix: -1.15 (1.31), residues: 14 sheet: -1.05 (0.28), residues: 279 loop : -2.06 (0.30), residues: 413 *********************** REFINEMENT MACRO_CYCLE 4 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 123 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.576 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 117 average time/residue: 0.1640 time to fit residues: 25.4956 Evaluate side-chains 104 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0540 time to fit residues: 1.4352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 5758 Z= 0.327 Angle : 0.752 9.257 7832 Z= 0.386 Chirality : 0.050 0.410 875 Planarity : 0.006 0.066 1000 Dihedral : 6.105 26.249 775 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer Outliers : 1.78 % 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: -2.35 (0.30), residues: 706 helix: -1.25 (1.23), residues: 14 sheet: -1.03 (0.28), residues: 279 loop : -2.00 (0.30), residues: 413 *********************** REFINEMENT MACRO_CYCLE 5 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 119 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 0.648 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.1684 time to fit residues: 25.5617 Evaluate side-chains 106 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0580 time to fit residues: 1.5607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 115 GLN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5758 Z= 0.186 Angle : 0.728 8.831 7832 Z= 0.369 Chirality : 0.049 0.361 875 Planarity : 0.005 0.063 1000 Dihedral : 5.725 28.771 775 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer Outliers : 1.62 % 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: -2.15 (0.30), residues: 706 helix: -1.13 (1.28), residues: 14 sheet: -0.77 (0.30), residues: 268 loop : -1.95 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 6 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 144 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 141 average time/residue: 0.1755 time to fit residues: 32.3655 Evaluate side-chains 114 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0576 time to fit residues: 1.2997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 5758 Z= 0.329 Angle : 0.770 9.974 7832 Z= 0.394 Chirality : 0.050 0.379 875 Planarity : 0.006 0.064 1000 Dihedral : 5.980 30.396 775 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.19 (0.30), residues: 706 helix: -1.08 (1.30), residues: 14 sheet: -0.90 (0.29), residues: 280 loop : -1.91 (0.30), residues: 412 *********************** REFINEMENT MACRO_CYCLE 7 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: 10 poor density : 110 time to evaluate : 0.668 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 119 average time/residue: 0.1702 time to fit residues: 26.6575 Evaluate side-chains 110 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 103 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0613 time to fit residues: 1.6076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 5758 Z= 0.279 Angle : 0.759 10.220 7832 Z= 0.389 Chirality : 0.050 0.371 875 Planarity : 0.005 0.063 1000 Dihedral : 5.978 28.164 775 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer Outliers : 0.97 % 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: -2.04 (0.31), residues: 706 helix: -1.06 (1.31), residues: 14 sheet: -0.87 (0.28), residues: 300 loop : -1.77 (0.31), residues: 392 *********************** REFINEMENT MACRO_CYCLE 8 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 119 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 117 average time/residue: 0.1776 time to fit residues: 27.1188 Evaluate side-chains 108 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0567 time to fit residues: 1.1730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 50.0000 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 5758 Z= 0.377 Angle : 0.788 10.829 7832 Z= 0.406 Chirality : 0.051 0.389 875 Planarity : 0.006 0.065 1000 Dihedral : 6.230 29.879 775 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer Outliers : 0.65 % 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: -2.17 (0.31), residues: 706 helix: -1.08 (1.31), residues: 14 sheet: -1.00 (0.28), residues: 309 loop : -1.82 (0.32), residues: 383 *********************** REFINEMENT MACRO_CYCLE 9 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 114 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.701 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 0.1723 time to fit residues: 25.6358 Evaluate side-chains 111 residues out of total 617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0535 time to fit residues: 0.9623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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-1.21rc1-5044/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: 58.6721 > 50: distance: 20 - 26: 7.554 distance: 26 - 27: 39.126 distance: 28 - 33: 18.201 distance: 30 - 31: 29.682 distance: 33 - 34: 23.411 distance: 34 - 35: 20.260 distance: 34 - 37: 31.437 distance: 35 - 36: 35.439 distance: 35 - 39: 4.900 distance: 37 - 38: 24.164 distance: 40 - 41: 12.495 distance: 41 - 42: 9.769 distance: 41 - 43: 11.576 distance: 43 - 44: 17.226 distance: 44 - 45: 10.766 distance: 44 - 47: 10.851 distance: 45 - 46: 17.642 distance: 45 - 50: 41.091 distance: 47 - 48: 12.854 distance: 47 - 49: 20.620 distance: 50 - 51: 20.832 distance: 50 - 144: 20.472 distance: 51 - 52: 36.962 distance: 51 - 54: 23.422 distance: 52 - 53: 39.332 distance: 53 - 141: 22.743 distance: 54 - 55: 22.846 distance: 55 - 56: 17.200 distance: 55 - 57: 33.211 distance: 56 - 58: 15.506 distance: 57 - 59: 34.175 distance: 58 - 59: 13.529 distance: 60 - 61: 26.333 distance: 61 - 62: 38.083 distance: 61 - 64: 7.157 distance: 62 - 63: 18.874 distance: 62 - 67: 12.974 distance: 64 - 65: 15.017 distance: 64 - 66: 24.656 distance: 67 - 68: 21.647 distance: 68 - 71: 20.032 distance: 69 - 70: 20.905 distance: 69 - 78: 30.099 distance: 71 - 72: 27.845 distance: 72 - 73: 19.854 distance: 72 - 74: 29.710 distance: 73 - 75: 22.154 distance: 74 - 76: 33.952 distance: 75 - 77: 25.530 distance: 76 - 77: 24.584 distance: 78 - 79: 5.181 distance: 78 - 84: 20.413 distance: 79 - 80: 17.598 distance: 79 - 82: 14.081 distance: 80 - 81: 14.277 distance: 80 - 85: 21.429 distance: 82 - 83: 23.262 distance: 83 - 84: 28.075 distance: 85 - 86: 8.499 distance: 86 - 87: 15.518 distance: 86 - 89: 10.531 distance: 87 - 88: 13.387 distance: 87 - 90: 30.518 distance: 90 - 91: 3.920 distance: 90 - 120: 17.779 distance: 91 - 92: 19.891 distance: 91 - 94: 9.051 distance: 92 - 93: 25.180 distance: 92 - 97: 27.847 distance: 94 - 95: 32.703 distance: 94 - 96: 43.289