Starting phenix.real_space_refine on Fri Aug 2 16:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qsn_18637/08_2024/8qsn_18637.cif" } resolution = 3.54 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= -0.001 sd= 0.013 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 20 5.16 5 C 2377 2.51 5 N 573 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3579 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3579 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 18, 'TRANS': 445} Chain breaks: 3 Time building chain proxies: 2.66, per 1000 atoms: 0.74 Number of scatterers: 3579 At special positions: 0 Unit cell: (80.465, 70.015, 65.835, 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 20 16.00 O 609 8.00 N 573 7.00 C 2377 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: 1.52 Conformation dependent library (CDL) restraints added in 586.4 milliseconds 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 846 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 1 sheets defined 83.4% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 33 through 57 removed outlier: 4.287A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 70 through 98 removed outlier: 3.899A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 102 through 118 Processing helix chain 'A' and resid 156 through 183 removed outlier: 4.226A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.629A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.818A pdb=" N THR A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 246 removed outlier: 3.931A pdb=" N GLY A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.638A pdb=" N VAL A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 273 Processing helix chain 'A' and resid 297 through 305 removed outlier: 3.954A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 305 " --> pdb=" O MET A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 347 removed outlier: 3.942A pdb=" N VAL A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix removed outlier: 3.691A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 365 through 366 No H-bonds generated for 'chain 'A' and resid 365 through 366' Processing helix chain 'A' and resid 367 through 396 removed outlier: 3.958A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Proline residue: A 382 - end of helix removed outlier: 5.109A pdb=" N ASP A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.528A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 removed outlier: 4.034A pdb=" N TRP A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 484 through 510 Processing helix chain 'A' and resid 531 through 560 removed outlier: 3.573A pdb=" N HIS A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 439 281 hydrogen bonds defined for protein. 837 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: 0.97 Time building geometry restraints manager: 1.67 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: 1081 1.34 - 1.46: 817 1.46 - 1.58: 1743 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 3672 Sorted by residual: bond pdb=" CB PRO A 399 " pdb=" CG PRO A 399 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.11e-01 bond pdb=" CA ILE A 329 " pdb=" C ILE A 329 " ideal model delta sigma weight residual 1.523 1.531 -0.008 9.20e-03 1.18e+04 7.12e-01 bond pdb=" C VAL A 246 " pdb=" O VAL A 246 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.67e-01 bond pdb=" CB PRO A 306 " pdb=" CG PRO A 306 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.05e-01 bond pdb=" N VAL A 322 " pdb=" CA VAL A 322 " ideal model delta sigma weight residual 1.463 1.470 -0.007 1.18e-02 7.18e+03 4.00e-01 ... (remaining 3667 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.07: 97 107.07 - 113.80: 2051 113.80 - 120.53: 1489 120.53 - 127.26: 1307 127.26 - 133.99: 41 Bond angle restraints: 4985 Sorted by residual: angle pdb=" C PHE A 247 " pdb=" N ILE A 248 " pdb=" CA ILE A 248 " ideal model delta sigma weight residual 121.97 125.78 -3.81 1.80e+00 3.09e-01 4.48e+00 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 113.00 110.27 2.73 1.30e+00 5.92e-01 4.42e+00 angle pdb=" N GLU A 309 " pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 110.80 115.23 -4.43 2.13e+00 2.20e-01 4.32e+00 angle pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.79e+00 angle pdb=" N ALA A 468 " pdb=" CA ALA A 468 " pdb=" C ALA A 468 " ideal model delta sigma weight residual 111.02 113.92 -2.90 1.52e+00 4.33e-01 3.64e+00 ... (remaining 4980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.62: 1970 14.62 - 29.24: 99 29.24 - 43.87: 29 43.87 - 58.49: 8 58.49 - 73.11: 2 Dihedral angle restraints: 2108 sinusoidal: 785 harmonic: 1323 Sorted by residual: dihedral pdb=" CA THR A 308 " pdb=" C THR A 308 " pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta harmonic sigma weight residual -180.00 -163.82 -16.18 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ARG A 33 " pdb=" CB ARG A 33 " pdb=" CG ARG A 33 " pdb=" CD ARG A 33 " ideal model delta sinusoidal sigma weight residual -60.00 -115.47 55.47 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA ARG A 104 " pdb=" CB ARG A 104 " pdb=" CG ARG A 104 " pdb=" CD ARG A 104 " ideal model delta sinusoidal sigma weight residual 180.00 127.75 52.25 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 2105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 389 0.025 - 0.050: 100 0.050 - 0.075: 55 0.075 - 0.101: 24 0.101 - 0.126: 6 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 571 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 238 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL A 238 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL A 238 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 239 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 239 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C VAL A 239 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL A 239 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 240 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 237 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE A 237 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 238 " -0.009 2.00e-02 2.50e+03 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 887 2.80 - 3.32: 3828 3.32 - 3.85: 5935 3.85 - 4.37: 6627 4.37 - 4.90: 11289 Nonbonded interactions: 28566 Sorted by model distance: nonbonded pdb=" O LEU A 264 " pdb=" OG SER A 267 " model vdw 2.269 3.040 nonbonded pdb=" O ILE A 461 " pdb=" OG SER A 464 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O GLY A 499 " model vdw 2.305 3.040 nonbonded pdb=" O LYS A 262 " pdb=" OG1 THR A 265 " model vdw 2.316 3.040 nonbonded pdb=" O CYS A 242 " pdb=" OG SER A 245 " model vdw 2.326 3.040 ... (remaining 28561 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.670 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.002 0.045 3672 Z= 0.125 Angle : 0.482 5.910 4985 Z= 0.259 Chirality : 0.034 0.126 574 Planarity : 0.004 0.029 611 Dihedral : 10.371 73.110 1262 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.75 % Allowed : 6.17 % Favored : 90.08 % 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: 2.22 (0.41), residues: 456 helix: 2.29 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -1.69 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 332 HIS 0.001 0.000 HIS A 348 PHE 0.009 0.001 PHE A 198 TYR 0.006 0.001 TYR A 52 ARG 0.001 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 171 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6367 (mtm-85) REVERT: A 44 GLU cc_start: 0.9074 (tp30) cc_final: 0.8872 (tp30) REVERT: A 47 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 91 PHE cc_start: 0.8834 (m-80) cc_final: 0.8615 (m-10) REVERT: A 198 PHE cc_start: 0.9062 (t80) cc_final: 0.8784 (t80) REVERT: A 200 TRP cc_start: 0.9108 (t60) cc_final: 0.8457 (t60) REVERT: A 313 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 342 TYR cc_start: 0.8828 (m-10) cc_final: 0.8493 (m-80) REVERT: A 369 LEU cc_start: 0.8668 (mt) cc_final: 0.8262 (mt) REVERT: A 427 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8093 (mt) REVERT: A 451 LEU cc_start: 0.9283 (tp) cc_final: 0.9027 (mp) REVERT: A 454 GLN cc_start: 0.8598 (tp40) cc_final: 0.8199 (tp40) REVERT: A 457 GLN cc_start: 0.7851 (pt0) cc_final: 0.6235 (pt0) REVERT: A 474 GLU cc_start: 0.8866 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 535 TYR cc_start: 0.8685 (t80) cc_final: 0.8193 (t80) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.1664 time to fit residues: 35.7945 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 427 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN ** A 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3672 Z= 0.209 Angle : 0.721 10.088 4985 Z= 0.340 Chirality : 0.040 0.157 574 Planarity : 0.005 0.051 611 Dihedral : 5.720 54.712 502 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.49 % Allowed : 18.77 % Favored : 77.75 % 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: 2.36 (0.40), residues: 456 helix: 2.37 (0.27), residues: 362 sheet: None (None), residues: 0 loop : -1.82 (0.58), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 69 HIS 0.003 0.001 HIS A 521 PHE 0.036 0.002 PHE A 417 TYR 0.013 0.002 TYR A 477 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6566 (ptp-170) REVERT: A 44 GLU cc_start: 0.9375 (tp30) cc_final: 0.9098 (tp30) REVERT: A 47 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 91 PHE cc_start: 0.8879 (m-80) cc_final: 0.8637 (m-10) REVERT: A 200 TRP cc_start: 0.9083 (t60) cc_final: 0.8393 (t60) REVERT: A 235 LEU cc_start: 0.9549 (mt) cc_final: 0.8983 (tp) REVERT: A 301 MET cc_start: 0.5932 (tpt) cc_final: 0.5677 (tmm) REVERT: A 309 GLU cc_start: 0.8861 (pm20) cc_final: 0.8258 (pm20) REVERT: A 331 TYR cc_start: 0.8992 (t80) cc_final: 0.8491 (t80) REVERT: A 427 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8450 (mt) REVERT: A 451 LEU cc_start: 0.9296 (tp) cc_final: 0.9038 (mp) REVERT: A 465 GLU cc_start: 0.8568 (tp30) cc_final: 0.8308 (tp30) REVERT: A 535 TYR cc_start: 0.8855 (t80) cc_final: 0.8418 (t80) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.1117 time to fit residues: 17.3092 Evaluate side-chains 105 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.0970 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3672 Z= 0.184 Angle : 0.701 11.263 4985 Z= 0.327 Chirality : 0.040 0.162 574 Planarity : 0.005 0.055 611 Dihedral : 5.751 54.791 500 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.83 % Allowed : 21.18 % Favored : 73.99 % 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: 2.11 (0.40), residues: 456 helix: 2.14 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -1.87 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.001 0.000 HIS A 521 PHE 0.044 0.002 PHE A 372 TYR 0.015 0.001 TYR A 335 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6565 (ptp-170) REVERT: A 91 PHE cc_start: 0.8884 (m-80) cc_final: 0.8656 (m-10) REVERT: A 200 TRP cc_start: 0.9101 (t60) cc_final: 0.8418 (t60) REVERT: A 301 MET cc_start: 0.6242 (tpt) cc_final: 0.5991 (tmm) REVERT: A 307 PHE cc_start: 0.3829 (OUTLIER) cc_final: 0.3528 (m-80) REVERT: A 331 TYR cc_start: 0.9034 (t80) cc_final: 0.8609 (t80) REVERT: A 413 MET cc_start: 0.8904 (tmm) cc_final: 0.8650 (tmm) REVERT: A 427 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8523 (mt) REVERT: A 451 LEU cc_start: 0.9270 (tp) cc_final: 0.9040 (mp) REVERT: A 458 TYR cc_start: 0.8942 (m-80) cc_final: 0.8721 (m-80) REVERT: A 474 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8165 (mt-10) REVERT: A 489 MET cc_start: 0.9511 (tpp) cc_final: 0.9297 (tpp) REVERT: A 535 TYR cc_start: 0.8872 (t80) cc_final: 0.8455 (t80) outliers start: 18 outliers final: 9 residues processed: 114 average time/residue: 0.1111 time to fit residues: 16.6671 Evaluate side-chains 106 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 532 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3672 Z= 0.178 Angle : 0.652 10.770 4985 Z= 0.314 Chirality : 0.040 0.158 574 Planarity : 0.005 0.046 611 Dihedral : 5.923 55.198 500 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 7.24 % Allowed : 20.64 % Favored : 72.12 % 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: 1.99 (0.40), residues: 456 helix: 2.03 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.77 (0.65), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.001 0.000 HIS A 559 PHE 0.051 0.002 PHE A 372 TYR 0.018 0.001 TYR A 215 ARG 0.005 0.000 ARG A 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 912 Ramachandran restraints generated. 456 Oldfield, 0 Emsley, 456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 101 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6528 (ptp-170) REVERT: A 200 TRP cc_start: 0.9168 (t60) cc_final: 0.8486 (t60) REVERT: A 301 MET cc_start: 0.6296 (tpt) cc_final: 0.6022 (tmm) REVERT: A 307 PHE cc_start: 0.3836 (OUTLIER) cc_final: 0.3543 (m-80) REVERT: A 310 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 331 TYR cc_start: 0.9086 (t80) cc_final: 0.8689 (t80) REVERT: A 427 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8597 (mt) REVERT: A 432 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 474 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 535 TYR cc_start: 0.8875 (t80) cc_final: 0.8533 (t80) outliers start: 27 outliers final: 14 residues processed: 120 average time/residue: 0.1194 time to fit residues: 18.7149 Evaluate side-chains 109 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 CYS Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.4989 > 50: distance: 12 - 35: 6.773 distance: 17 - 46: 24.651 distance: 24 - 54: 19.791 distance: 28 - 35: 4.456 distance: 29 - 62: 20.771 distance: 35 - 36: 14.118 distance: 36 - 37: 14.141 distance: 36 - 39: 18.333 distance: 37 - 38: 20.677 distance: 37 - 46: 18.915 distance: 38 - 70: 33.142 distance: 39 - 40: 8.584 distance: 40 - 41: 16.979 distance: 41 - 42: 8.217 distance: 43 - 44: 3.656 distance: 46 - 47: 24.778 distance: 47 - 48: 44.829 distance: 47 - 50: 30.880 distance: 48 - 49: 11.793 distance: 48 - 54: 16.248 distance: 50 - 51: 12.709 distance: 51 - 52: 28.487 distance: 51 - 53: 26.620 distance: 54 - 55: 27.718 distance: 55 - 56: 13.182 distance: 55 - 58: 29.485 distance: 56 - 57: 14.979 distance: 56 - 62: 34.371 distance: 58 - 59: 33.797 distance: 59 - 60: 18.525 distance: 59 - 61: 21.541 distance: 62 - 63: 3.476 distance: 63 - 64: 22.986 distance: 63 - 66: 14.335 distance: 64 - 65: 46.531 distance: 64 - 70: 40.259 distance: 66 - 67: 12.590 distance: 67 - 68: 4.375 distance: 67 - 69: 5.395 distance: 70 - 71: 17.049 distance: 71 - 72: 21.972 distance: 71 - 74: 38.638 distance: 72 - 73: 21.849 distance: 74 - 75: 15.545 distance: 74 - 76: 22.487 distance: 77 - 78: 5.299 distance: 78 - 79: 4.103 distance: 78 - 81: 55.485 distance: 79 - 80: 31.465 distance: 79 - 86: 30.733 distance: 81 - 82: 35.037 distance: 82 - 83: 34.052 distance: 83 - 84: 38.099 distance: 84 - 85: 12.823 distance: 86 - 87: 8.746 distance: 87 - 88: 23.774 distance: 87 - 90: 12.597 distance: 88 - 89: 19.628 distance: 88 - 95: 25.168 distance: 90 - 91: 16.672 distance: 91 - 92: 4.693 distance: 92 - 93: 9.468 distance: 95 - 96: 12.852 distance: 96 - 97: 9.212 distance: 96 - 99: 20.019 distance: 97 - 98: 16.551 distance: 97 - 104: 19.905 distance: 99 - 100: 28.839 distance: 100 - 101: 21.164 distance: 101 - 102: 5.416 distance: 102 - 103: 18.009 distance: 104 - 105: 30.692 distance: 105 - 106: 25.844 distance: 105 - 108: 16.308 distance: 106 - 107: 18.615 distance: 106 - 111: 28.840 distance: 108 - 109: 14.960 distance: 108 - 110: 35.958 distance: 111 - 112: 18.884 distance: 111 - 143: 27.109 distance: 112 - 113: 16.316 distance: 112 - 115: 27.774 distance: 113 - 114: 16.987 distance: 113 - 119: 8.795 distance: 114 - 140: 24.290 distance: 115 - 116: 15.113 distance: 115 - 117: 10.245 distance: 116 - 118: 13.759