Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 23:31:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y7w_33672/10_2023/7y7w_33672_updated.pdb" } resolution = 2.4 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= 0.002 sd= 0.098 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: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2844 2.51 5 N 655 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ASP 395": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4310 Unusual residues: {' CL': 1, ' NA': 2, 'ABU': 1, 'NAG': 3} Classifications: {'peptide': 529, 'undetermined': 7, 'water': 48} Link IDs: {'PTRANS': 22, 'TRANS': 506, None: 55} Not linked: pdbres="ILE A 577 " pdbres="ABU A 701 " Not linked: pdbres="ABU A 701 " pdbres="NAG A 702 " Not linked: pdbres="NAG A 702 " pdbres="NAG A 703 " Not linked: pdbres="NAG A 703 " pdbres="NAG A 704 " Not linked: pdbres="NAG A 704 " pdbres=" NA A 705 " ... (remaining 50 not shown) Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.81, per 1000 atoms: 0.65 Number of scatterers: 4310 At special positions: 0 Unit cell: (67.115, 72.5275, 95.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 Na 2 11.00 O 774 8.00 N 655 7.00 C 2844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 173 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 181 " " NAG A 703 " - " ASN A 176 " " NAG A 704 " - " ASN A 184 " Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 574.9 milliseconds 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 64 through 67 No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.627A pdb=" N ILE A 84 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Proline residue: A 85 - end of helix Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 120 through 154 removed outlier: 4.455A pdb=" N GLY A 124 " --> pdb=" O MET A 121 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TYR A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 240 through 258 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.579A pdb=" N SER A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.580A pdb=" N TYR A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 349 Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 373 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 378 through 411 removed outlier: 3.720A pdb=" N ASP A 395 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 No H-bonds generated for 'chain 'A' and resid 413 through 416' Processing helix chain 'A' and resid 420 through 438 removed outlier: 4.701A pdb=" N SER A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 453 Processing helix chain 'A' and resid 457 through 473 removed outlier: 3.760A pdb=" N ILE A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 503 through 517 Processing helix chain 'A' and resid 531 through 558 removed outlier: 4.996A pdb=" N LEU A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Proline residue: A 549 - end of helix removed outlier: 3.550A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.460A pdb=" N VAL A 569 " --> pdb=" O GLN A 565 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 621 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: 1.08 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 620 1.29 - 1.42: 1312 1.42 - 1.55: 2407 1.55 - 1.68: 0 1.68 - 1.81: 54 Bond restraints: 4393 Sorted by residual: bond pdb=" C ASP A 395 " pdb=" O ASP A 395 " ideal model delta sigma weight residual 1.237 1.165 0.072 1.19e-02 7.06e+03 3.64e+01 bond pdb=" C PHE A 53 " pdb=" O PHE A 53 " ideal model delta sigma weight residual 1.237 1.183 0.053 1.19e-02 7.06e+03 2.01e+01 bond pdb=" C SER A 396 " pdb=" O SER A 396 " ideal model delta sigma weight residual 1.237 1.186 0.050 1.17e-02 7.31e+03 1.85e+01 bond pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 1.237 1.193 0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.75e+00 ... (remaining 4388 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 90 105.83 - 112.88: 2238 112.88 - 119.94: 1636 119.94 - 127.00: 1946 127.00 - 134.06: 72 Bond angle restraints: 5982 Sorted by residual: angle pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " ideal model delta sigma weight residual 112.60 119.69 -7.09 1.00e+00 1.00e+00 5.03e+01 angle pdb=" OG1 THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 109.30 120.42 -11.12 2.00e+00 2.50e-01 3.09e+01 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 105.81 5.55 1.09e+00 8.42e-01 2.59e+01 angle pdb=" CA ILE A 394 " pdb=" C ILE A 394 " pdb=" O ILE A 394 " ideal model delta sigma weight residual 120.85 115.79 5.06 1.06e+00 8.90e-01 2.28e+01 angle pdb=" CA THR A 406 " pdb=" CB THR A 406 " pdb=" CG2 THR A 406 " ideal model delta sigma weight residual 110.50 118.58 -8.08 1.70e+00 3.46e-01 2.26e+01 ... (remaining 5977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2120 17.95 - 35.90: 251 35.90 - 53.86: 63 53.86 - 71.81: 15 71.81 - 89.76: 6 Dihedral angle restraints: 2455 sinusoidal: 932 harmonic: 1523 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 173 " pdb=" CB CYS A 173 " ideal model delta sinusoidal sigma weight residual -86.00 -49.63 -36.37 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" N MET A 200 " pdb=" CA MET A 200 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR A 453 " pdb=" C TYR A 453 " pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 663 0.277 - 0.554: 1 0.554 - 0.831: 0 0.831 - 1.108: 0 1.108 - 1.385: 2 Chirality restraints: 666 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 1.17 1.38 2.00e-01 2.50e+01 4.80e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 184 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.54e+01 chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 176 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.78 0.38 2.00e-01 2.50e+01 3.55e+00 ... (remaining 663 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 181 " -0.101 2.00e-02 2.50e+03 1.71e-01 3.66e+02 pdb=" CG ASN A 181 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN A 181 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN A 181 " 0.307 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 184 " 0.134 2.00e-02 2.50e+03 1.38e-01 2.40e+02 pdb=" CG ASN A 184 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 184 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 184 " -0.203 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 176 " 0.064 2.00e-02 2.50e+03 6.39e-02 5.11e+01 pdb=" CG ASN A 176 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 176 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 176 " -0.098 2.00e-02 2.50e+03 pdb=" C1 NAG A 703 " 0.077 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 40 2.51 - 3.10: 3270 3.10 - 3.70: 7039 3.70 - 4.30: 10496 4.30 - 4.90: 16729 Nonbonded interactions: 37574 Sorted by model distance: nonbonded pdb=" O HOH A 805 " pdb=" O HOH A 828 " model vdw 1.907 2.440 nonbonded pdb=" O HOH A 801 " pdb=" O HOH A 806 " model vdw 2.000 2.440 nonbonded pdb=" OE1 GLU A 101 " pdb=" O HOH A 801 " model vdw 2.008 2.440 nonbonded pdb=" O LEU A 298 " pdb=" O HOH A 802 " model vdw 2.030 2.440 nonbonded pdb=" OG1 THR A 290 " pdb=" O HOH A 803 " model vdw 2.045 2.440 ... (remaining 37569 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 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: 0.430 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: 0.020 Extract box with map and model: 1.880 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.260 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:10.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 4393 Z= 0.358 Angle : 0.777 11.117 5982 Z= 0.474 Chirality : 0.084 1.385 666 Planarity : 0.005 0.042 725 Dihedral : 17.458 89.759 1486 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.11 % Allowed : 26.73 % Favored : 72.16 % 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: 0.06 (0.36), residues: 527 helix: 0.63 (0.26), residues: 376 sheet: None (None), residues: 0 loop : -1.32 (0.50), residues: 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.465 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 65 average time/residue: 1.2176 time to fit residues: 82.2235 Evaluate side-chains 54 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4393 Z= 0.188 Angle : 0.595 8.812 5982 Z= 0.303 Chirality : 0.043 0.300 666 Planarity : 0.004 0.036 725 Dihedral : 4.690 19.922 576 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.23 % Allowed : 20.49 % Favored : 75.28 % 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: 0.68 (0.37), residues: 527 helix: 1.19 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.34 (0.47), residues: 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.486 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 73 average time/residue: 0.9940 time to fit residues: 76.0049 Evaluate side-chains 60 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.6645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 57 optimal weight: 50.0000 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.191 Angle : 0.562 7.973 5982 Z= 0.289 Chirality : 0.044 0.301 666 Planarity : 0.004 0.033 725 Dihedral : 4.560 19.557 576 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.12 % Allowed : 20.49 % Favored : 74.39 % 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: 0.77 (0.37), residues: 527 helix: 1.27 (0.27), residues: 374 sheet: None (None), residues: 0 loop : -1.38 (0.46), residues: 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.504 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 78 average time/residue: 0.9209 time to fit residues: 75.4622 Evaluate side-chains 71 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.5652 time to fit residues: 1.8123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 56 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8290 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4393 Z= 0.203 Angle : 0.542 7.744 5982 Z= 0.286 Chirality : 0.044 0.278 666 Planarity : 0.004 0.034 725 Dihedral : 4.541 19.696 576 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.57 % Allowed : 20.27 % Favored : 74.16 % 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: 0.84 (0.37), residues: 527 helix: 1.32 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -1.38 (0.47), residues: 151 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1054 Ramachandran restraints generated. 527 Oldfield, 0 Emsley, 527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 54 time to evaluate : 0.488 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 75 average time/residue: 0.8588 time to fit residues: 67.7645 Evaluate side-chains 70 residues out of total 449 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.0707 time to fit residues: 0.8240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 71.7028 > 50: distance: 27 - 32: 33.439 distance: 32 - 33: 40.642 distance: 33 - 34: 69.341 distance: 33 - 36: 42.350 distance: 34 - 35: 56.497 distance: 34 - 39: 43.899 distance: 36 - 37: 28.140 distance: 36 - 38: 49.323 distance: 39 - 40: 17.196 distance: 40 - 41: 51.511 distance: 40 - 43: 65.048 distance: 41 - 42: 39.965 distance: 41 - 47: 40.633 distance: 43 - 44: 49.448 distance: 44 - 46: 50.689 distance: 47 - 48: 29.244 distance: 47 - 53: 10.155 distance: 48 - 49: 42.281 distance: 48 - 51: 38.648 distance: 49 - 50: 42.273 distance: 49 - 54: 34.095 distance: 51 - 52: 40.854 distance: 52 - 53: 40.643 distance: 55 - 56: 39.559 distance: 55 - 58: 37.414 distance: 56 - 57: 59.475 distance: 56 - 68: 56.125 distance: 58 - 59: 56.524 distance: 59 - 60: 65.290 distance: 59 - 61: 54.749 distance: 60 - 62: 7.107 distance: 61 - 63: 26.350 distance: 61 - 64: 53.462 distance: 62 - 63: 9.756 distance: 63 - 65: 8.131 distance: 64 - 66: 31.000 distance: 65 - 67: 26.697 distance: 66 - 67: 14.658 distance: 68 - 69: 56.688 distance: 69 - 70: 29.678 distance: 69 - 72: 8.293 distance: 70 - 71: 16.251 distance: 70 - 77: 40.742 distance: 72 - 73: 38.625 distance: 73 - 74: 44.527 distance: 74 - 75: 56.342 distance: 75 - 76: 60.214 distance: 78 - 79: 41.005 distance: 78 - 81: 39.824 distance: 79 - 80: 38.796 distance: 79 - 86: 40.610 distance: 81 - 82: 3.500 distance: 82 - 83: 38.640 distance: 83 - 84: 40.244 distance: 83 - 85: 44.394 distance: 86 - 87: 56.727 distance: 87 - 88: 57.074 distance: 88 - 89: 55.385 distance: 90 - 91: 39.237 distance: 91 - 141: 36.295 distance: 93 - 94: 53.426 distance: 93 - 96: 39.583 distance: 94 - 95: 39.729 distance: 94 - 100: 51.855 distance: 96 - 97: 14.672 distance: 97 - 98: 57.484 distance: 97 - 99: 42.102 distance: 100 - 101: 41.227 distance: 101 - 102: 56.902 distance: 101 - 104: 55.083 distance: 102 - 103: 41.064 distance: 102 - 108: 67.748 distance: 104 - 105: 41.135 distance: 105 - 106: 39.430 distance: 105 - 107: 41.287 distance: 108 - 109: 37.105 distance: 108 - 114: 55.808 distance: 109 - 110: 50.575 distance: 109 - 112: 39.265 distance: 110 - 111: 31.447 distance: 110 - 115: 29.493 distance: 112 - 113: 42.027 distance: 113 - 114: 44.244