Starting phenix.real_space_refine on Wed Jan 17 19:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/01_2024/6pzt_20537.pdb" } resolution = 3.46 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= 0.058 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 24 5.16 5 C 3914 2.51 5 N 1026 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6062 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3031 Classifications: {'peptide': 466} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 126} Link IDs: {'PTRANS': 15, 'TRANS': 450} Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 233 Chain: "A" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3031 Classifications: {'peptide': 466} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 126} Link IDs: {'PTRANS': 15, 'TRANS': 450} Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 6, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 12, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 233 Time building chain proxies: 3.94, per 1000 atoms: 0.65 Number of scatterers: 6062 At special positions: 0 Unit cell: (82.95, 101.85, 87.15, 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 24 16.00 O 1098 8.00 N 1026 7.00 C 3914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 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: 2.58 Conformation dependent library (CDL) restraints added in 1.5 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 301 through 315 removed outlier: 4.364A pdb=" N PHE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER B 309 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 342 removed outlier: 3.789A pdb=" N VAL B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 360 Processing helix chain 'B' and resid 361 through 398 removed outlier: 3.702A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.461A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.104A pdb=" N ILE B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 486 through 495 Processing helix chain 'B' and resid 496 through 499 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 514 through 516 No H-bonds generated for 'chain 'B' and resid 514 through 516' Processing helix chain 'B' and resid 517 through 542 removed outlier: 3.699A pdb=" N GLY B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.790A pdb=" N LYS B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 597 removed outlier: 3.528A pdb=" N SER B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 632 removed outlier: 4.069A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.510A pdb=" N GLY B 644 " --> pdb=" O PHE B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 668 removed outlier: 4.130A pdb=" N ILE B 668 " --> pdb=" O GLY B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 698 Proline residue: B 676 - end of helix Processing helix chain 'B' and resid 712 through 730 removed outlier: 3.901A pdb=" N SER B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 752 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.363A pdb=" N PHE A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N SER A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 342 removed outlier: 3.789A pdb=" N VAL A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 361 through 398 removed outlier: 3.702A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 4.460A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 454 removed outlier: 4.104A pdb=" N ILE A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 517 through 542 removed outlier: 3.698A pdb=" N GLY A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.790A pdb=" N LYS A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.529A pdb=" N SER A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 632 removed outlier: 4.069A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.511A pdb=" N GLY A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 668 removed outlier: 4.130A pdb=" N ILE A 668 " --> pdb=" O GLY A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 698 Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 712 through 730 removed outlier: 3.901A pdb=" N SER A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 492 hydrogen bonds defined for protein. 1440 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: 1.76 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1990 1.34 - 1.46: 1608 1.46 - 1.58: 2564 1.58 - 1.70: 0 1.70 - 1.82: 32 Bond restraints: 6194 Sorted by residual: bond pdb=" CB TRP A 310 " pdb=" CG TRP A 310 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.09e+00 bond pdb=" CB TRP B 310 " pdb=" CG TRP B 310 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB THR B 328 " pdb=" CG2 THR B 328 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 bond pdb=" CB THR A 328 " pdb=" CG2 THR A 328 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB TYR A 468 " pdb=" CG TYR A 468 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.20e-02 2.07e+03 1.24e+00 ... (remaining 6189 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.84: 142 106.84 - 113.67: 3496 113.67 - 120.51: 2519 120.51 - 127.34: 2279 127.34 - 134.18: 58 Bond angle restraints: 8494 Sorted by residual: angle pdb=" C PHE B 599 " pdb=" N THR B 600 " pdb=" CA THR B 600 " ideal model delta sigma weight residual 120.58 125.14 -4.56 1.32e+00 5.74e-01 1.20e+01 angle pdb=" N VAL B 347 " pdb=" CA VAL B 347 " pdb=" C VAL B 347 " ideal model delta sigma weight residual 112.50 108.27 4.23 1.39e+00 5.18e-01 9.25e+00 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 112.50 108.35 4.15 1.39e+00 5.18e-01 8.92e+00 angle pdb=" C GLY A 585 " pdb=" N LEU A 586 " pdb=" CA LEU A 586 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.81e+00 angle pdb=" C GLY B 585 " pdb=" N LEU B 586 " pdb=" CA LEU B 586 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.79e+00 ... (remaining 8489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.65: 2990 10.65 - 21.31: 327 21.31 - 31.96: 90 31.96 - 42.61: 39 42.61 - 53.27: 16 Dihedral angle restraints: 3462 sinusoidal: 888 harmonic: 2574 Sorted by residual: dihedral pdb=" CA LEU B 698 " pdb=" C LEU B 698 " pdb=" N ALA B 699 " pdb=" CA ALA B 699 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU A 698 " pdb=" C LEU A 698 " pdb=" N ALA A 699 " pdb=" CA ALA A 699 " ideal model delta harmonic sigma weight residual -180.00 -153.01 -26.99 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL A 557 " pdb=" C VAL A 557 " pdb=" N THR A 558 " pdb=" CA THR A 558 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 3459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 444 0.027 - 0.054: 319 0.054 - 0.081: 165 0.081 - 0.108: 51 0.108 - 0.134: 37 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CB VAL A 673 " pdb=" CA VAL A 673 " pdb=" CG1 VAL A 673 " pdb=" CG2 VAL A 673 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CB VAL B 673 " pdb=" CA VAL B 673 " pdb=" CG1 VAL B 673 " pdb=" CG2 VAL B 673 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA PRO B 601 " pdb=" N PRO B 601 " pdb=" C PRO B 601 " pdb=" CB PRO B 601 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1013 not shown) Planarity restraints: 1104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 600 " 0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO A 601 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 601 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 601 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 600 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO B 601 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 601 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 601 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 371 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C ILE B 371 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE B 371 " -0.009 2.00e-02 2.50e+03 pdb=" N PHE B 372 " -0.008 2.00e-02 2.50e+03 ... (remaining 1101 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 171 2.68 - 3.23: 7210 3.23 - 3.79: 10019 3.79 - 4.34: 12017 4.34 - 4.90: 19143 Nonbonded interactions: 48560 Sorted by model distance: nonbonded pdb=" OD2 ASP B 448 " pdb=" OG SER B 597 " model vdw 2.120 2.440 nonbonded pdb=" OD2 ASP A 448 " pdb=" OG SER A 597 " model vdw 2.121 2.440 nonbonded pdb=" O SER A 609 " pdb=" OG SER A 613 " model vdw 2.185 2.440 nonbonded pdb=" O SER B 609 " pdb=" OG SER B 613 " model vdw 2.185 2.440 nonbonded pdb=" O LEU B 336 " pdb=" OG SER B 339 " model vdw 2.224 2.440 ... (remaining 48555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.410 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: 5.960 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.170 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.007 0.045 6194 Z= 0.474 Angle : 0.746 6.741 8494 Z= 0.425 Chirality : 0.047 0.134 1016 Planarity : 0.004 0.042 1104 Dihedral : 11.587 50.244 1826 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.43 % Allowed : 10.30 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.25), residues: 928 helix: -1.36 (0.17), residues: 628 sheet: None (None), residues: 0 loop : -3.49 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.000 HIS A 398 PHE 0.016 0.002 PHE A 488 TYR 0.018 0.002 TYR A 751 ARG 0.004 0.001 ARG A 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 0.765 Fit side-chains REVERT: B 358 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8174 (mtm180) REVERT: B 433 LYS cc_start: 0.6335 (mmmt) cc_final: 0.5809 (tttt) REVERT: B 436 ILE cc_start: 0.8072 (mm) cc_final: 0.7690 (mt) REVERT: B 562 ASN cc_start: 0.7878 (p0) cc_final: 0.7305 (p0) REVERT: A 358 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8171 (mtm180) REVERT: A 433 LYS cc_start: 0.6590 (mmmt) cc_final: 0.6211 (tttt) REVERT: A 562 ASN cc_start: 0.7850 (p0) cc_final: 0.7338 (p0) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1616 time to fit residues: 27.3503 Evaluate side-chains 89 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 0.0040 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- 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: 0.7453 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6194 Z= 0.189 Angle : 0.604 7.252 8494 Z= 0.323 Chirality : 0.042 0.127 1016 Planarity : 0.005 0.059 1104 Dihedral : 5.066 21.759 962 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.08 % Allowed : 16.31 % Favored : 79.61 % 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: -0.75 (0.28), residues: 928 helix: 0.55 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.91 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 733 HIS 0.001 0.000 HIS A 695 PHE 0.011 0.001 PHE B 465 TYR 0.010 0.001 TYR A 584 ARG 0.006 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: B 292 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.7090 (tt) REVERT: B 294 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7731 (tpp80) REVERT: B 358 ARG cc_start: 0.8523 (ttm170) cc_final: 0.7985 (mtm180) REVERT: B 429 GLU cc_start: 0.8243 (pt0) cc_final: 0.7984 (pm20) REVERT: B 433 LYS cc_start: 0.6441 (mmmt) cc_final: 0.5900 (tttt) REVERT: B 436 ILE cc_start: 0.8135 (mm) cc_final: 0.7737 (mt) REVERT: B 562 ASN cc_start: 0.7738 (p0) cc_final: 0.7344 (p0) REVERT: B 680 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 739 TYR cc_start: 0.8637 (m-80) cc_final: 0.8395 (m-80) REVERT: A 358 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8023 (mtm180) REVERT: A 433 LYS cc_start: 0.6581 (mmmt) cc_final: 0.6122 (tttt) REVERT: A 435 GLN cc_start: 0.7620 (tt0) cc_final: 0.7327 (tt0) REVERT: A 436 ILE cc_start: 0.7962 (mm) cc_final: 0.7570 (mt) outliers start: 19 outliers final: 8 residues processed: 127 average time/residue: 0.1676 time to fit residues: 28.4307 Evaluate side-chains 110 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 679 SER Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 679 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 69 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6194 Z= 0.190 Angle : 0.578 6.337 8494 Z= 0.310 Chirality : 0.042 0.118 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.765 19.690 962 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.94 % Allowed : 17.60 % Favored : 77.47 % 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: -0.23 (0.28), residues: 928 helix: 0.98 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -2.93 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.025 0.001 PHE B 659 TYR 0.006 0.001 TYR A 751 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 ARG cc_start: 0.8319 (tpp80) cc_final: 0.8098 (ttm170) REVERT: B 429 GLU cc_start: 0.8244 (pt0) cc_final: 0.7988 (pm20) REVERT: B 433 LYS cc_start: 0.6431 (mmmt) cc_final: 0.5905 (tttt) REVERT: B 436 ILE cc_start: 0.8130 (mm) cc_final: 0.7743 (mt) REVERT: B 523 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 562 ASN cc_start: 0.7820 (p0) cc_final: 0.7438 (p0) REVERT: B 680 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7470 (t0) REVERT: B 739 TYR cc_start: 0.8625 (m-80) cc_final: 0.8416 (m-80) REVERT: A 433 LYS cc_start: 0.6616 (mmmt) cc_final: 0.6138 (tttt) REVERT: A 436 ILE cc_start: 0.7970 (mm) cc_final: 0.7548 (mt) REVERT: A 562 ASN cc_start: 0.7847 (p0) cc_final: 0.7507 (p0) outliers start: 23 outliers final: 9 residues processed: 123 average time/residue: 0.1576 time to fit residues: 26.2673 Evaluate side-chains 110 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 584 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 680 ASN Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 620 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 50.417 > 50: distance: 10 - 27: 12.276 distance: 14 - 32: 29.107 distance: 19 - 39: 20.658 distance: 23 - 27: 15.223 distance: 24 - 44: 14.712 distance: 27 - 28: 19.087 distance: 28 - 29: 17.683 distance: 28 - 31: 16.146 distance: 29 - 32: 42.967 distance: 32 - 33: 12.899 distance: 33 - 34: 5.289 distance: 33 - 36: 5.146 distance: 34 - 35: 14.040 distance: 34 - 39: 20.403 distance: 35 - 56: 33.216 distance: 36 - 37: 37.371 distance: 36 - 38: 4.929 distance: 39 - 40: 10.951 distance: 40 - 41: 5.906 distance: 40 - 43: 12.260 distance: 41 - 42: 18.709 distance: 41 - 44: 13.205 distance: 42 - 64: 15.017 distance: 44 - 45: 16.385 distance: 45 - 46: 19.772 distance: 45 - 48: 23.972 distance: 46 - 47: 23.029 distance: 46 - 51: 11.995 distance: 47 - 76: 16.546 distance: 48 - 49: 31.614 distance: 48 - 50: 20.066 distance: 51 - 52: 16.492 distance: 52 - 53: 26.025 distance: 52 - 55: 8.716 distance: 53 - 54: 13.439 distance: 53 - 56: 12.378 distance: 54 - 83: 18.740 distance: 56 - 57: 6.709 distance: 57 - 58: 9.246 distance: 57 - 60: 5.041 distance: 58 - 59: 13.423 distance: 58 - 64: 19.861 distance: 59 - 90: 9.868 distance: 60 - 61: 7.939 distance: 61 - 62: 41.548 distance: 62 - 63: 4.716 distance: 64 - 65: 4.289 distance: 65 - 66: 4.759 distance: 65 - 68: 6.039 distance: 66 - 76: 4.391 distance: 67 - 94: 21.565 distance: 68 - 69: 3.376 distance: 69 - 70: 6.256 distance: 69 - 71: 8.319 distance: 70 - 72: 11.327 distance: 71 - 73: 11.086 distance: 72 - 74: 7.336 distance: 73 - 74: 5.752 distance: 74 - 75: 10.885 distance: 76 - 77: 12.219 distance: 77 - 78: 16.966 distance: 77 - 80: 5.463 distance: 78 - 79: 7.392 distance: 78 - 83: 13.357 distance: 79 - 101: 23.632 distance: 80 - 81: 28.583 distance: 80 - 82: 6.911 distance: 83 - 84: 9.761 distance: 84 - 85: 8.365 distance: 84 - 87: 10.976 distance: 85 - 86: 16.552 distance: 85 - 90: 20.550 distance: 86 - 106: 24.949 distance: 87 - 88: 16.916 distance: 87 - 89: 9.986 distance: 90 - 91: 3.816 distance: 91 - 92: 28.384 distance: 92 - 93: 15.623 distance: 92 - 94: 14.493 distance: 93 - 112: 13.923