Starting phenix.real_space_refine on Fri Dec 8 00:56:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vq5_32086/12_2023/7vq5_32086_updated.pdb" } resolution = 3.1 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= 0.005 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 34 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1155 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 13": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6315 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "B" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3162 Unusual residues: {'LMR': 1} Classifications: {'peptide': 400, 'undetermined': 1} Link IDs: {'PTRANS': 12, 'TRANS': 387, None: 1} Not linked: pdbres="MET B 405 " pdbres="LMR B 601 " Chain breaks: 1 Time building chain proxies: 4.15, per 1000 atoms: 0.66 Number of scatterers: 6315 At special positions: 0 Unit cell: (83.148, 90.246, 112.554, 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 34 16.00 O 1155 8.00 N 1052 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 20 through 40 removed outlier: 3.942A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 70 through 101 Processing helix chain 'A' and resid 105 through 126 removed outlier: 4.213A pdb=" N PHE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 135 through 150 Processing helix chain 'A' and resid 155 through 182 Processing helix chain 'A' and resid 188 through 213 Processing helix chain 'A' and resid 224 through 240 removed outlier: 5.024A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.568A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 307 through 329 Processing helix chain 'A' and resid 336 through 356 removed outlier: 3.800A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 398 Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.518A pdb=" N ILE B 7 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.560A pdb=" N ILE B 23 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 24 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 26 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 29 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 32 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 36 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 39 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 65 removed outlier: 3.523A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 101 removed outlier: 3.844A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 99 " --> pdb=" O HIS B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 126 removed outlier: 4.046A pdb=" N VAL B 111 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.026A pdb=" N THR B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.631A pdb=" N PHE B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 182 removed outlier: 3.715A pdb=" N MET B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 214 removed outlier: 3.812A pdb=" N ASP B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 212 " --> pdb=" O GLN B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.884A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.601A pdb=" N GLU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 290 removed outlier: 3.512A pdb=" N GLN B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 329 removed outlier: 3.724A pdb=" N LYS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N THR B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Proline residue: B 309 - end of helix removed outlier: 3.881A pdb=" N GLU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 356 removed outlier: 3.524A pdb=" N ASN B 343 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 365 through 398 removed outlier: 4.667A pdb=" N SER B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 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: 1.82 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1586 1.33 - 1.45: 1178 1.45 - 1.57: 3618 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6442 Sorted by residual: bond pdb=" C1 LMR B 601 " pdb=" C2 LMR B 601 " ideal model delta sigma weight residual 1.543 1.495 0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" C ILE B 53 " pdb=" O ILE B 53 " ideal model delta sigma weight residual 1.236 1.212 0.025 1.19e-02 7.06e+03 4.27e+00 bond pdb=" C ILE A 53 " pdb=" O ILE A 53 " ideal model delta sigma weight residual 1.236 1.212 0.024 1.19e-02 7.06e+03 4.09e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" C3 LMR B 601 " pdb=" C4 LMR B 601 " ideal model delta sigma weight residual 1.538 1.503 0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 6437 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.23: 125 106.23 - 113.19: 3618 113.19 - 120.16: 2582 120.16 - 127.12: 2317 127.12 - 134.09: 60 Bond angle restraints: 8702 Sorted by residual: angle pdb=" C GLU A 307 " pdb=" N THR A 308 " pdb=" CA THR A 308 " ideal model delta sigma weight residual 119.83 116.03 3.80 1.11e+00 8.12e-01 1.17e+01 angle pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" C TYR A 39 " ideal model delta sigma weight residual 111.36 114.89 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C GLU B 6 " pdb=" N ILE B 7 " pdb=" CA ILE B 7 " ideal model delta sigma weight residual 122.35 118.75 3.60 1.18e+00 7.18e-01 9.31e+00 angle pdb=" C THR A 132 " pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta sigma weight residual 122.42 118.05 4.37 1.55e+00 4.16e-01 7.96e+00 angle pdb=" C GLY B 260 " pdb=" N GLN B 261 " pdb=" CA GLN B 261 " ideal model delta sigma weight residual 124.31 128.72 -4.41 1.67e+00 3.59e-01 6.98e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3384 17.98 - 35.95: 405 35.95 - 53.93: 68 53.93 - 71.91: 5 71.91 - 89.89: 1 Dihedral angle restraints: 3863 sinusoidal: 1539 harmonic: 2324 Sorted by residual: dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual 180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TRP A 255 " pdb=" C TRP A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N GLU A 234 " pdb=" CA GLU A 234 " ideal model delta harmonic sigma weight residual 180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 3860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 783 0.054 - 0.108: 197 0.108 - 0.163: 15 0.163 - 0.217: 1 0.217 - 0.271: 1 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA TYR A 39 " pdb=" N TYR A 39 " pdb=" C TYR A 39 " pdb=" CB TYR A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA TYR A 40 " pdb=" N TYR A 40 " pdb=" C TYR A 40 " pdb=" CB TYR A 40 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA PRO B 258 " pdb=" N PRO B 258 " pdb=" C PRO B 258 " pdb=" CB PRO B 258 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 994 not shown) Planarity restraints: 1092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 257 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 258 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 18 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 19 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 200 " -0.013 2.00e-02 2.50e+03 1.02e-02 1.81e+00 pdb=" CG PHE B 200 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 200 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 200 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 200 " -0.003 2.00e-02 2.50e+03 ... (remaining 1089 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 97 2.67 - 3.23: 6486 3.23 - 3.78: 9477 3.78 - 4.34: 12885 4.34 - 4.90: 21474 Nonbonded interactions: 50419 Sorted by model distance: nonbonded pdb=" OH TYR B 236 " pdb=" OD1 ASP B 286 " model vdw 2.110 2.440 nonbonded pdb=" OE1 GLU B 246 " pdb=" NH2 ARG B 279 " model vdw 2.185 2.520 nonbonded pdb=" O ILE B 369 " pdb=" OG1 THR B 373 " model vdw 2.210 2.440 nonbonded pdb=" NH2 ARG B 80 " pdb=" O4A LMR B 601 " model vdw 2.242 2.520 nonbonded pdb=" NZ LYS B 133 " pdb=" OE1 GLU B 254 " model vdw 2.247 2.520 ... (remaining 50414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 405) } 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 individual isotropic 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.640 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 0.009 0.067 6442 Z= 0.591 Angle : 0.766 7.360 8702 Z= 0.446 Chirality : 0.046 0.271 997 Planarity : 0.004 0.043 1092 Dihedral : 14.845 89.886 2359 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.14 % Allowed : 12.36 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.25), residues: 792 helix: -1.79 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -4.38 (0.42), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 255 HIS 0.006 0.002 HIS B 259 PHE 0.023 0.002 PHE B 200 TYR 0.015 0.002 TYR A 271 ARG 0.005 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.711 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.2142 time to fit residues: 26.0701 Evaluate side-chains 76 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 95 HIS A 266 HIS A 289 ASN A 293 ASN A 340 HIS B 266 HIS ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6442 Z= 0.203 Angle : 0.493 5.487 8702 Z= 0.272 Chirality : 0.037 0.141 997 Planarity : 0.004 0.035 1092 Dihedral : 4.431 19.738 865 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.72 % Allowed : 13.79 % Favored : 84.48 % 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: -0.71 (0.29), residues: 792 helix: 0.13 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -3.29 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 255 HIS 0.003 0.001 HIS A 95 PHE 0.015 0.001 PHE A 206 TYR 0.020 0.002 TYR A 39 ARG 0.004 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.763 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.1779 time to fit residues: 22.4443 Evaluate side-chains 94 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0620 time to fit residues: 1.9359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 68.8875 > 50: distance: 51 - 69: 30.069 distance: 56 - 76: 21.171 distance: 65 - 69: 30.153 distance: 66 - 94: 22.112 distance: 69 - 70: 30.368 distance: 70 - 71: 21.770 distance: 70 - 73: 30.128 distance: 71 - 72: 23.972 distance: 71 - 76: 39.597 distance: 72 - 102: 58.415 distance: 73 - 74: 23.239 distance: 73 - 75: 22.260 distance: 76 - 77: 37.489 distance: 77 - 78: 14.642 distance: 77 - 80: 31.718 distance: 78 - 79: 31.157 distance: 78 - 85: 50.901 distance: 79 - 108: 53.044 distance: 80 - 81: 42.996 distance: 81 - 82: 20.342 distance: 82 - 83: 29.801 distance: 82 - 84: 14.937 distance: 85 - 86: 11.237 distance: 86 - 87: 28.769 distance: 86 - 89: 14.860 distance: 87 - 88: 4.997 distance: 87 - 94: 32.940 distance: 88 - 117: 32.806 distance: 89 - 90: 34.805 distance: 90 - 91: 40.229 distance: 91 - 92: 4.328 distance: 92 - 93: 39.271 distance: 94 - 95: 27.717 distance: 95 - 96: 39.844 distance: 95 - 98: 14.284 distance: 96 - 97: 19.550 distance: 96 - 102: 28.390 distance: 97 - 123: 17.155 distance: 98 - 99: 40.447 distance: 98 - 100: 28.299 distance: 99 - 101: 40.755 distance: 102 - 103: 46.530 distance: 103 - 104: 28.968 distance: 103 - 106: 18.323 distance: 104 - 105: 49.320 distance: 104 - 108: 42.982 distance: 105 - 130: 38.142 distance: 106 - 107: 45.308 distance: 108 - 109: 31.082 distance: 109 - 110: 51.996 distance: 109 - 112: 13.699 distance: 110 - 111: 51.265 distance: 110 - 117: 27.210 distance: 111 - 140: 55.266 distance: 112 - 113: 56.526 distance: 113 - 114: 25.005 distance: 114 - 115: 12.983 distance: 114 - 116: 5.503 distance: 117 - 118: 39.763 distance: 118 - 119: 38.122 distance: 118 - 121: 35.209 distance: 119 - 120: 39.716 distance: 119 - 123: 31.459 distance: 120 - 149: 36.249 distance: 121 - 122: 21.537 distance: 123 - 124: 23.718 distance: 124 - 125: 37.919 distance: 124 - 127: 41.774 distance: 125 - 126: 12.088 distance: 125 - 130: 33.469 distance: 126 - 156: 29.995 distance: 127 - 128: 12.032 distance: 127 - 129: 5.681 distance: 130 - 131: 25.063 distance: 135 - 136: 18.496 distance: 135 - 137: 34.562 distance: 136 - 138: 33.328 distance: 137 - 139: 20.284 distance: 138 - 139: 25.890 distance: 141 - 144: 7.258 distance: 142 - 149: 35.336 distance: 143 - 166: 37.375 distance: 144 - 145: 34.243 distance: 145 - 146: 31.739 distance: 146 - 147: 31.649 distance: 146 - 148: 17.363