Starting phenix.real_space_refine on Fri Dec 8 00:10:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/12_2023/6pzt_20537.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/12_2023/6pzt_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_20537/12_2023/6pzt_20537.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/12_2023/6pzt_20537.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/12_2023/6pzt_20537.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzt_20537/12_2023/6pzt_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-1.21rc1-5172/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: 3.71, per 1000 atoms: 0.61 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: 2.26 Conformation dependent library (CDL) restraints added in 1.3 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: 0.62 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: 1.78 Time building geometry restraints manager: 2.47 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.000 Extract box with map and model: 5.920 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.330 Find NCS groups from input model: 0.340 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- 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 : 0.672 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.1538 time to fit residues: 25.9835 Evaluate side-chains 87 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8378 ------------------------------------------------------------------------------- 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: 0.4980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7461 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6194 Z= 0.197 Angle : 0.611 6.852 8494 Z= 0.328 Chirality : 0.043 0.124 1016 Planarity : 0.005 0.059 1104 Dihedral : 5.118 22.532 962 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.86 % Allowed : 16.31 % Favored : 79.83 % 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: -0.82 (0.28), residues: 928 helix: 0.48 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.88 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.001 0.000 HIS A 695 PHE 0.011 0.001 PHE B 465 TYR 0.009 0.001 TYR A 584 ARG 0.005 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 129 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.693 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.1736 time to fit residues: 29.3143 Evaluate side-chains 101 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0624 time to fit residues: 1.7044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6194 Z= 0.181 Angle : 0.580 6.855 8494 Z= 0.310 Chirality : 0.042 0.127 1016 Planarity : 0.004 0.065 1104 Dihedral : 4.764 19.327 962 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.00 % Allowed : 19.53 % 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: -0.14 (0.28), residues: 928 helix: 1.02 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.74 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.025 0.001 PHE B 659 TYR 0.010 0.001 TYR A 354 ARG 0.006 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 126 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.658 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 122 average time/residue: 0.1594 time to fit residues: 26.3647 Evaluate side-chains 100 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.704 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0707 time to fit residues: 1.2791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.0470 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 0.0870 chunk 74 optimal weight: 6.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 298 ASN B 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6194 Z= 0.175 Angle : 0.571 7.811 8494 Z= 0.304 Chirality : 0.042 0.120 1016 Planarity : 0.005 0.066 1104 Dihedral : 4.574 17.639 962 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.72 % Allowed : 20.39 % Favored : 74.89 % 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: 0.09 (0.29), residues: 928 helix: 1.18 (0.20), residues: 648 sheet: None (None), residues: 0 loop : -2.73 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.034 0.001 PHE A 659 TYR 0.008 0.001 TYR B 686 ARG 0.005 0.001 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 4 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 132 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.627 Fit side-chains outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 0.1633 time to fit residues: 27.2630 Evaluate side-chains 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1671 time to fit residues: 2.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 36 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 22 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6194 Z= 0.175 Angle : 0.586 9.591 8494 Z= 0.306 Chirality : 0.042 0.120 1016 Planarity : 0.004 0.065 1104 Dihedral : 4.408 17.616 962 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.43 % Allowed : 20.82 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 928 helix: 1.14 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.028 0.001 PHE A 659 TYR 0.009 0.001 TYR A 686 ARG 0.006 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 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 122 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 106 time to evaluate : 0.718 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 115 average time/residue: 0.1496 time to fit residues: 24.1019 Evaluate side-chains 101 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0690 time to fit residues: 1.6851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6194 Z= 0.220 Angle : 0.592 6.632 8494 Z= 0.316 Chirality : 0.043 0.145 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.479 17.448 962 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.00 % Allowed : 21.67 % Favored : 75.32 % 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: 0.35 (0.28), residues: 928 helix: 1.29 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -2.41 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.026 0.001 PHE A 659 TYR 0.010 0.001 TYR B 584 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 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 113 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.657 Fit side-chains outliers start: 14 outliers final: 3 residues processed: 108 average time/residue: 0.1481 time to fit residues: 22.3170 Evaluate side-chains 93 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0572 time to fit residues: 1.1830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6194 Z= 0.195 Angle : 0.589 9.469 8494 Z= 0.311 Chirality : 0.043 0.178 1016 Planarity : 0.004 0.065 1104 Dihedral : 4.425 16.520 962 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.36 % Allowed : 23.39 % Favored : 74.25 % 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: 0.26 (0.28), residues: 928 helix: 1.19 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.49 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.024 0.001 PHE A 659 TYR 0.012 0.001 TYR A 584 ARG 0.005 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 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 105 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.646 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 100 average time/residue: 0.1472 time to fit residues: 20.6210 Evaluate side-chains 92 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0568 time to fit residues: 1.1627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 80 optimal weight: 0.0060 chunk 84 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6194 Z= 0.178 Angle : 0.586 10.204 8494 Z= 0.309 Chirality : 0.042 0.181 1016 Planarity : 0.005 0.065 1104 Dihedral : 4.385 17.773 962 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.50 % Allowed : 24.25 % Favored : 74.25 % 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: 0.32 (0.29), residues: 928 helix: 1.22 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.49 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.027 0.001 PHE A 659 TYR 0.011 0.001 TYR A 686 ARG 0.007 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 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 112 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.699 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 108 average time/residue: 0.1578 time to fit residues: 23.5626 Evaluate side-chains 97 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.695 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0649 time to fit residues: 1.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 ASN A 376 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6194 Z= 0.200 Angle : 0.612 11.785 8494 Z= 0.318 Chirality : 0.043 0.176 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.361 17.463 962 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.15 % Allowed : 25.32 % Favored : 72.53 % 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: 0.35 (0.28), residues: 928 helix: 1.23 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.45 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.001 0.001 HIS A 695 PHE 0.031 0.001 PHE A 659 TYR 0.010 0.001 TYR A 686 ARG 0.002 0.001 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 9 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 104 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.674 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 0.1630 time to fit residues: 21.6500 Evaluate side-chains 95 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0695 time to fit residues: 1.1884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6194 Z= 0.180 Angle : 0.630 12.113 8494 Z= 0.320 Chirality : 0.043 0.190 1016 Planarity : 0.004 0.065 1104 Dihedral : 4.284 16.927 962 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.86 % Allowed : 26.82 % Favored : 72.32 % 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: 0.38 (0.28), residues: 928 helix: 1.26 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.45 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.028 0.001 PHE A 659 TYR 0.010 0.001 TYR A 584 ARG 0.001 0.000 ARG B 351 ********************** REFINEMENT MACRO_CYCLE 10 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 109 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.710 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 105 average time/residue: 0.1577 time to fit residues: 22.8248 Evaluate side-chains 99 residues out of total 758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0562 time to fit residues: 0.9816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.129372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109312 restraints weight = 12514.768| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.77 r_work: 0.3415 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6194 Z= 0.192 Angle : 0.630 11.286 8494 Z= 0.321 Chirality : 0.043 0.165 1016 Planarity : 0.004 0.064 1104 Dihedral : 4.263 16.714 962 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.50 % Allowed : 26.82 % Favored : 71.67 % 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: 0.42 (0.29), residues: 928 helix: 1.28 (0.20), residues: 666 sheet: None (None), residues: 0 loop : -2.42 (0.40), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.001 0.001 HIS B 695 PHE 0.029 0.001 PHE A 659 TYR 0.010 0.001 TYR A 686 ARG 0.004 0.001 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1429.78 seconds wall clock time: 26 minutes 38.42 seconds (1598.42 seconds total)