Starting phenix.real_space_refine on Sat Aug 3 06:12:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6coy_7544/08_2024/6coy_7544.cif" } resolution = 3.36 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= 0.003 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 4 4.86 5 C 4776 2.51 5 N 1130 2.21 5 O 1188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 205": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7156 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3576 Classifications: {'peptide': 465} Link IDs: {'PTRANS': 25, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.89, per 1000 atoms: 0.68 Number of scatterers: 7156 At special positions: 0 Unit cell: (110.21, 77.25, 76.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 58 16.00 O 1188 8.00 N 1130 7.00 C 4776 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: 2.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 78.8% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 116 through 152 Processing helix chain 'A' and resid 156 through 183 Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 190 through 199 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 231 through 250 Processing helix chain 'A' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 299 through 323 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 379 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 419 through 428 Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN A 445 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 475 Processing helix chain 'A' and resid 483 through 503 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 541 through 551 Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 576 through 585 Processing helix chain 'B' and resid 117 through 152 Processing helix chain 'B' and resid 156 through 183 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 231 through 250 Processing helix chain 'B' and resid 263 through 280 removed outlier: 3.538A pdb=" N THR B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 299 through 323 Processing helix chain 'B' and resid 344 through 346 No H-bonds generated for 'chain 'B' and resid 344 through 346' Processing helix chain 'B' and resid 347 through 379 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.707A pdb=" N LYS B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 419 through 428 Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 439 through 450 removed outlier: 6.892A pdb=" N GLN B 445 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 475 Processing helix chain 'B' and resid 483 through 503 Processing helix chain 'B' and resid 521 through 538 Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 576 through 585 Processing sheet with id=AA1, first strand: chain 'A' and resid 296 through 298 Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 510 through 512 551 hydrogen bonds defined for protein. 1551 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: 2.28 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1096 1.31 - 1.43: 2014 1.43 - 1.56: 4140 1.56 - 1.68: 4 1.68 - 1.81: 98 Bond restraints: 7352 Sorted by residual: bond pdb=" CB ILE A 556 " pdb=" CG1 ILE A 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB ILE B 556 " pdb=" CG1 ILE B 556 " ideal model delta sigma weight residual 1.530 1.377 0.153 2.00e-02 2.50e+03 5.83e+01 bond pdb=" CB HIS B 538 " pdb=" CG HIS B 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB HIS A 538 " pdb=" CG HIS A 538 " ideal model delta sigma weight residual 1.497 1.424 0.073 1.40e-02 5.10e+03 2.74e+01 bond pdb=" CB ILE B 553 " pdb=" CG1 ILE B 553 " ideal model delta sigma weight residual 1.530 1.431 0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 7347 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.24: 220 105.24 - 112.41: 3618 112.41 - 119.58: 2560 119.58 - 126.76: 3528 126.76 - 133.93: 80 Bond angle restraints: 10006 Sorted by residual: angle pdb=" C THR B 281 " pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C THR A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.24 127.81 -8.57 1.04e+00 9.25e-01 6.80e+01 angle pdb=" C LEU A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C LEU B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.47 128.00 -8.53 1.16e+00 7.43e-01 5.41e+01 angle pdb=" C PHE B 341 " pdb=" N PRO B 342 " pdb=" CA PRO B 342 " ideal model delta sigma weight residual 119.56 125.93 -6.37 1.01e+00 9.80e-01 3.97e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4126 17.23 - 34.46: 86 34.46 - 51.69: 18 51.69 - 68.91: 18 68.91 - 86.14: 6 Dihedral angle restraints: 4254 sinusoidal: 1592 harmonic: 2662 Sorted by residual: dihedral pdb=" CA THR B 432 " pdb=" C THR B 432 " pdb=" N TRP B 433 " pdb=" CA TRP B 433 " ideal model delta harmonic sigma weight residual 180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA THR A 432 " pdb=" C THR A 432 " pdb=" N TRP A 433 " pdb=" CA TRP A 433 " ideal model delta harmonic sigma weight residual -180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" C TYR B 393 " pdb=" N TYR B 393 " pdb=" CA TYR B 393 " pdb=" CB TYR B 393 " ideal model delta harmonic sigma weight residual -122.60 -130.59 7.99 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 4251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 684 0.069 - 0.139: 342 0.139 - 0.208: 102 0.208 - 0.278: 34 0.278 - 0.347: 8 Chirality restraints: 1170 Sorted by residual: chirality pdb=" CA PRO A 407 " pdb=" N PRO A 407 " pdb=" C PRO A 407 " pdb=" CB PRO A 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 407 " pdb=" N PRO B 407 " pdb=" C PRO B 407 " pdb=" CB PRO B 407 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PRO B 558 " pdb=" N PRO B 558 " pdb=" C PRO B 558 " pdb=" CB PRO B 558 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1167 not shown) Planarity restraints: 1224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 590 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO B 591 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 590 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO A 591 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 591 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO A 591 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 485 " 0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO B 486 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 486 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 486 " 0.056 5.00e-02 4.00e+02 ... (remaining 1221 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1662 2.77 - 3.31: 7383 3.31 - 3.84: 12334 3.84 - 4.37: 14469 4.37 - 4.90: 24411 Nonbonded interactions: 60259 Sorted by model distance: nonbonded pdb=" N GLN A 185 " pdb=" OE1 GLN A 185 " model vdw 2.242 3.120 nonbonded pdb=" N GLN B 185 " pdb=" OE1 GLN B 185 " model vdw 2.242 3.120 nonbonded pdb=" CB GLU A 291 " pdb=" OE1 GLU A 291 " model vdw 2.449 2.752 nonbonded pdb=" CB GLU B 291 " pdb=" OE1 GLU B 291 " model vdw 2.449 2.752 nonbonded pdb=" OE1 GLU B 291 " pdb=" OG1 THR B 539 " model vdw 2.501 3.040 ... (remaining 60254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.100 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.380 Find NCS groups from input model: 0.210 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.020 0.153 7352 Z= 1.323 Angle : 1.425 13.192 10006 Z= 0.978 Chirality : 0.091 0.347 1170 Planarity : 0.014 0.150 1224 Dihedral : 10.542 86.142 2546 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.43 % Allowed : 2.82 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: -0.30 (0.25), residues: 922 helix: 0.29 (0.18), residues: 668 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP A 322 HIS 0.007 0.002 HIS B 436 PHE 0.029 0.005 PHE A 547 TYR 0.044 0.010 TYR B 296 ARG 0.006 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1349 time to fit residues: 24.3538 Evaluate side-chains 82 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS A 436 HIS A 538 HIS B 369 HIS B 436 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7352 Z= 0.261 Angle : 0.614 6.443 10006 Z= 0.330 Chirality : 0.043 0.149 1170 Planarity : 0.008 0.072 1224 Dihedral : 4.178 15.153 978 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.57 % Allowed : 5.64 % Favored : 92.78 % 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: 1.95 (0.28), residues: 922 helix: 1.99 (0.19), residues: 672 sheet: None (None), residues: 0 loop : -0.65 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.003 0.001 HIS A 451 PHE 0.030 0.002 PHE A 547 TYR 0.011 0.002 TYR B 589 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 ASP cc_start: 0.8099 (t0) cc_final: 0.7608 (t0) REVERT: A 346 LYS cc_start: 0.8154 (mttt) cc_final: 0.7922 (mptt) REVERT: B 325 ASP cc_start: 0.8095 (t0) cc_final: 0.7606 (t0) REVERT: B 346 LYS cc_start: 0.8153 (mttt) cc_final: 0.7922 (mptt) outliers start: 12 outliers final: 8 residues processed: 136 average time/residue: 0.1457 time to fit residues: 28.8176 Evaluate side-chains 112 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 410 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 74 optimal weight: 0.0030 chunk 82 optimal weight: 0.6980 chunk 28 optimal weight: 0.0770 chunk 67 optimal weight: 0.3980 overall best weight: 0.2748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7352 Z= 0.176 Angle : 0.520 6.506 10006 Z= 0.276 Chirality : 0.041 0.146 1170 Planarity : 0.006 0.063 1224 Dihedral : 3.822 13.705 978 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.57 % Allowed : 8.27 % Favored : 90.16 % 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: 2.90 (0.28), residues: 922 helix: 2.77 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -0.38 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 469 HIS 0.002 0.001 HIS B 379 PHE 0.029 0.001 PHE B 547 TYR 0.007 0.001 TYR B 137 ARG 0.002 0.000 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7378 (t80) REVERT: A 325 ASP cc_start: 0.8147 (t0) cc_final: 0.7678 (t0) REVERT: B 262 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7377 (t80) REVERT: B 325 ASP cc_start: 0.8148 (t0) cc_final: 0.7683 (t0) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.1448 time to fit residues: 22.8508 Evaluate side-chains 101 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7352 Z= 0.248 Angle : 0.534 5.793 10006 Z= 0.280 Chirality : 0.042 0.143 1170 Planarity : 0.006 0.066 1224 Dihedral : 3.726 13.502 978 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 9.32 % Favored : 88.32 % 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: 2.78 (0.28), residues: 922 helix: 2.72 (0.19), residues: 666 sheet: None (None), residues: 0 loop : -0.63 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 469 HIS 0.003 0.001 HIS A 451 PHE 0.028 0.002 PHE B 547 TYR 0.010 0.001 TYR B 146 ARG 0.003 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8014 (ttpt) cc_final: 0.7559 (ptmm) REVERT: A 325 ASP cc_start: 0.8265 (t0) cc_final: 0.7771 (t0) REVERT: B 204 LYS cc_start: 0.8015 (ttpt) cc_final: 0.7561 (ptmm) REVERT: B 325 ASP cc_start: 0.8265 (t0) cc_final: 0.7771 (t0) outliers start: 18 outliers final: 16 residues processed: 118 average time/residue: 0.1430 time to fit residues: 25.1467 Evaluate side-chains 116 residues out of total 762 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 VAL 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: 70.6485 > 50: distance: 53 - 56: 21.019 distance: 56 - 57: 27.449 distance: 57 - 58: 24.416 distance: 58 - 59: 17.382 distance: 58 - 60: 38.709 distance: 60 - 61: 26.620 distance: 61 - 62: 5.971 distance: 61 - 64: 21.709 distance: 62 - 63: 21.539 distance: 62 - 69: 24.421 distance: 64 - 65: 24.205 distance: 65 - 66: 16.960 distance: 66 - 67: 12.270 distance: 66 - 68: 22.594 distance: 69 - 70: 15.863 distance: 70 - 73: 27.011 distance: 71 - 72: 39.481 distance: 71 - 77: 40.221 distance: 73 - 74: 25.760 distance: 74 - 75: 12.270 distance: 74 - 76: 57.685 distance: 77 - 78: 69.552 distance: 78 - 79: 45.778 distance: 78 - 81: 21.548 distance: 80 - 112: 44.253 distance: 81 - 82: 35.369 distance: 82 - 83: 56.895 distance: 83 - 84: 56.664 distance: 85 - 86: 16.695 distance: 85 - 91: 24.225 distance: 86 - 87: 24.990 distance: 87 - 88: 15.469 distance: 87 - 92: 13.964 distance: 88 - 117: 38.224 distance: 89 - 90: 33.058 distance: 90 - 91: 8.575 distance: 92 - 93: 14.088 distance: 93 - 94: 30.044 distance: 93 - 96: 41.502 distance: 94 - 95: 27.777 distance: 94 - 103: 42.978 distance: 95 - 125: 53.720 distance: 96 - 97: 39.161 distance: 97 - 98: 52.936 distance: 98 - 99: 3.892 distance: 99 - 100: 39.801 distance: 100 - 102: 17.521 distance: 103 - 104: 19.861 distance: 104 - 105: 20.359 distance: 104 - 107: 60.600 distance: 105 - 112: 21.349 distance: 106 - 131: 36.177 distance: 107 - 108: 5.456 distance: 108 - 109: 4.445 distance: 109 - 110: 10.581 distance: 109 - 111: 10.598 distance: 112 - 113: 37.910 distance: 115 - 138: 37.834 distance: 117 - 118: 43.837 distance: 118 - 119: 36.824 distance: 118 - 121: 34.261 distance: 119 - 120: 29.474 distance: 119 - 125: 33.273 distance: 120 - 146: 29.421 distance: 121 - 122: 35.440 distance: 121 - 123: 31.245 distance: 122 - 124: 21.314 distance: 125 - 126: 4.693 distance: 126 - 127: 56.999 distance: 126 - 129: 38.167 distance: 127 - 128: 25.638 distance: 127 - 131: 28.113