Starting phenix.real_space_refine on Thu Jul 18 17:24:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggx_40024/07_2024/8ggx_40024.cif" } resolution = 3.6 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= 0.019 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 13 5.16 5 C 1402 2.51 5 N 332 2.21 5 O 360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 122": "OE1" <-> "OE2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 192": "OD1" <-> "OD2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "R PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2107 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2092 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 79 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 1.26 Number of scatterers: 2107 At special positions: 0 Unit cell: (55.5328, 84.1669, 63.3421, 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 13 16.00 O 360 8.00 N 332 7.00 C 1402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.756A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY R 37 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 Processing helix chain 'R' and resid 68 through 96 removed outlier: 4.181A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 4.182A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N HIS R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.008A pdb=" N CYS R 106 " --> pdb=" O GLY R 102 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU R 107 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.814A pdb=" N ALA R 150 " --> pdb=" O THR R 146 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.617A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.778A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 299 removed outlier: 4.490A pdb=" N LEU R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.052A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.610A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 322 removed outlier: 3.696A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 317 through 322' Processing helix chain 'R' and resid 322 through 327 removed outlier: 3.515A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 340 150 hydrogen bonds defined for protein. 447 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: 0.55 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 638 1.34 - 1.46: 542 1.46 - 1.58: 965 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 2163 Sorted by residual: bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.573 -0.050 2.00e-02 2.50e+03 6.13e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.441 -0.047 2.00e-02 2.50e+03 5.63e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.565 -0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.22e+00 ... (remaining 2158 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.42: 60 107.42 - 114.10: 1243 114.10 - 120.78: 1046 120.78 - 127.46: 593 127.46 - 134.14: 27 Bond angle restraints: 2969 Sorted by residual: angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.31 116.98 3.33 1.52e+00 4.33e-01 4.80e+00 angle pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 112.63 118.20 -5.57 3.00e+00 1.11e-01 3.45e+00 angle pdb=" CA VAL R 295 " pdb=" C VAL R 295 " pdb=" N HIS R 296 " ideal model delta sigma weight residual 117.28 119.25 -1.97 1.16e+00 7.43e-01 2.89e+00 angle pdb=" N HIS R 296 " pdb=" CA HIS R 296 " pdb=" CB HIS R 296 " ideal model delta sigma weight residual 110.28 112.78 -2.50 1.55e+00 4.16e-01 2.60e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 115.65 -4.76 3.00e+00 1.11e-01 2.51e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 1113 17.53 - 35.05: 92 35.05 - 52.58: 19 52.58 - 70.11: 2 70.11 - 87.63: 2 Dihedral angle restraints: 1228 sinusoidal: 400 harmonic: 828 Sorted by residual: dihedral pdb=" CA GLN R 299 " pdb=" C GLN R 299 " pdb=" N ASP R 300 " pdb=" CA ASP R 300 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA GLN R 197 " pdb=" C GLN R 197 " pdb=" N ALA R 198 " pdb=" CA ALA R 198 " ideal model delta harmonic sigma weight residual 180.00 163.04 16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU R 180 " pdb=" CG GLU R 180 " pdb=" CD GLU R 180 " pdb=" OE1 GLU R 180 " ideal model delta sinusoidal sigma weight residual 0.00 -87.63 87.63 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 1225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 230 0.034 - 0.067: 101 0.067 - 0.101: 25 0.101 - 0.135: 3 0.135 - 0.168: 1 Chirality restraints: 360 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.07e-01 chirality pdb=" CA TYR R 326 " pdb=" N TYR R 326 " pdb=" C TYR R 326 " pdb=" CB TYR R 326 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.99e-01 chirality pdb=" CA LEU R 287 " pdb=" N LEU R 287 " pdb=" C LEU R 287 " pdb=" CB LEU R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.11 2.00e-01 2.50e+01 2.76e-01 ... (remaining 357 not shown) Planarity restraints: 362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 173 " -0.010 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP R 173 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP R 173 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 173 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 173 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 173 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 173 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 173 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO R 168 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 137 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.16e+00 pdb=" N PRO R 138 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO R 138 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 138 " -0.015 5.00e-02 4.00e+02 ... (remaining 359 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1031 2.97 - 3.45: 2339 3.45 - 3.94: 3154 3.94 - 4.42: 3299 4.42 - 4.90: 5590 Nonbonded interactions: 15413 Sorted by model distance: nonbonded pdb=" OE1 GLU R 180 " pdb=" N ALA R 181 " model vdw 2.489 2.520 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.507 2.440 nonbonded pdb=" OE2 GLU R 107 " pdb=" OH TYR R 174 " model vdw 2.558 2.440 nonbonded pdb=" O TRP R 158 " pdb=" OG SER R 161 " model vdw 2.629 2.440 nonbonded pdb=" N THR R 146 " pdb=" O THR R 146 " model vdw 2.646 2.496 ... (remaining 15408 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=0.00 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: 1.670 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.004 0.054 2163 Z= 0.228 Angle : 0.544 5.572 2969 Z= 0.293 Chirality : 0.039 0.168 360 Planarity : 0.004 0.030 362 Dihedral : 14.257 87.632 690 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.20 (0.51), residues: 277 helix: 2.53 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -1.62 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 173 HIS 0.003 0.001 HIS R 178 PHE 0.014 0.001 PHE R 336 TYR 0.006 0.001 TYR R 326 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.274 Fit side-chains REVERT: R 192 ASP cc_start: 0.7667 (p0) cc_final: 0.7135 (p0) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1069 time to fit residues: 6.6040 Evaluate side-chains 38 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.0070 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2163 Z= 0.185 Angle : 0.504 5.351 2969 Z= 0.284 Chirality : 0.038 0.128 360 Planarity : 0.004 0.029 362 Dihedral : 4.560 16.991 309 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.48 % Allowed : 10.45 % Favored : 86.07 % 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: 2.07 (0.52), residues: 277 helix: 2.44 (0.36), residues: 203 sheet: None (None), residues: 0 loop : -1.83 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 PHE 0.012 0.001 PHE R 104 TYR 0.018 0.002 TYR R 185 ARG 0.000 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.225 Fit side-chains REVERT: R 185 TYR cc_start: 0.7920 (m-80) cc_final: 0.7642 (m-80) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.0959 time to fit residues: 5.3891 Evaluate side-chains 42 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2163 Z= 0.182 Angle : 0.499 5.338 2969 Z= 0.279 Chirality : 0.038 0.127 360 Planarity : 0.003 0.024 362 Dihedral : 4.566 16.522 309 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.98 % Allowed : 14.93 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.51), residues: 277 helix: 2.40 (0.36), residues: 204 sheet: None (None), residues: 0 loop : -1.92 (0.66), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE R 104 TYR 0.014 0.002 TYR R 185 ARG 0.000 0.000 ARG R 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.200 Fit side-chains REVERT: R 185 TYR cc_start: 0.8059 (m-80) cc_final: 0.7632 (m-80) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1002 time to fit residues: 5.3806 Evaluate side-chains 43 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 37 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 169 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2163 Z= 0.215 Angle : 0.516 5.342 2969 Z= 0.290 Chirality : 0.038 0.128 360 Planarity : 0.004 0.027 362 Dihedral : 4.589 16.633 309 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.48 % Allowed : 13.93 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.51), residues: 277 helix: 2.28 (0.36), residues: 205 sheet: None (None), residues: 0 loop : -2.04 (0.65), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 173 HIS 0.004 0.001 HIS R 178 PHE 0.008 0.001 PHE R 193 TYR 0.012 0.002 TYR R 326 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.223 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 0.0925 time to fit residues: 5.3258 Evaluate side-chains 42 residues out of total 248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2958 > 50: distance: 2 - 22: 8.189 distance: 6 - 26: 4.629 distance: 11 - 34: 19.220 distance: 15 - 22: 6.665 distance: 16 - 41: 26.886 distance: 22 - 23: 5.115 distance: 23 - 24: 4.269 distance: 24 - 25: 8.203 distance: 24 - 26: 3.003 distance: 25 - 49: 20.028 distance: 26 - 27: 6.746 distance: 27 - 28: 7.901 distance: 27 - 30: 6.619 distance: 29 - 56: 16.719 distance: 30 - 31: 9.049 distance: 31 - 32: 3.767 distance: 31 - 33: 7.674 distance: 34 - 35: 7.058 distance: 35 - 36: 18.099 distance: 35 - 38: 12.826 distance: 36 - 37: 20.164 distance: 36 - 41: 28.169 distance: 37 - 64: 16.746 distance: 38 - 39: 9.165 distance: 38 - 40: 7.882 distance: 41 - 42: 33.358 distance: 42 - 43: 21.915 distance: 42 - 45: 22.459 distance: 43 - 44: 8.842 distance: 43 - 49: 10.608 distance: 44 - 71: 11.441 distance: 45 - 46: 19.248 distance: 46 - 47: 24.186 distance: 46 - 48: 4.773 distance: 49 - 50: 9.517 distance: 50 - 51: 4.256 distance: 50 - 53: 4.313 distance: 51 - 52: 6.167 distance: 52 - 76: 9.182 distance: 53 - 54: 8.856 distance: 53 - 55: 5.505 distance: 56 - 57: 4.463 distance: 57 - 60: 4.471 distance: 58 - 59: 3.227 distance: 59 - 84: 11.259 distance: 60 - 61: 6.562 distance: 60 - 62: 17.765 distance: 61 - 63: 8.452 distance: 64 - 65: 5.175 distance: 65 - 68: 5.308 distance: 67 - 89: 6.683 distance: 68 - 69: 8.035 distance: 68 - 70: 8.068 distance: 71 - 72: 4.888 distance: 72 - 73: 7.363 distance: 72 - 75: 6.880 distance: 73 - 74: 6.960 distance: 73 - 76: 3.230 distance: 77 - 78: 3.623 distance: 77 - 80: 3.654 distance: 78 - 79: 4.801 distance: 80 - 81: 5.380 distance: 80 - 82: 7.018 distance: 81 - 83: 9.238 distance: 84 - 85: 5.880 distance: 85 - 86: 3.350 distance: 85 - 88: 5.799 distance: 86 - 87: 13.699