Starting phenix.real_space_refine on Tue Nov 19 09:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9chs_45600/11_2024/9chs_45600.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6292 2.51 5 N 1568 2.21 5 O 1600 1.98 5 H 9596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19104 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "B" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "C" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Chain: "D" Number of atoms: 4776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4776 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 3 Time building chain proxies: 9.23, per 1000 atoms: 0.48 Number of scatterers: 19104 At special positions: 0 Unit cell: (123.9, 122.85, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1600 8.00 N 1568 7.00 C 6292 6.00 H 9596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.98 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 404 through 432 Proline residue: A 426 - end of helix Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.897A pdb=" N ILE A 467 " --> pdb=" O PHE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 496 Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 517 through 525 removed outlier: 3.748A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 530 Processing helix chain 'A' and resid 531 through 538 removed outlier: 3.918A pdb=" N VAL A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 Processing helix chain 'A' and resid 545 through 576 Processing helix chain 'A' and resid 584 through 593 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 634 through 667 removed outlier: 3.593A pdb=" N ALA A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 688 Processing helix chain 'A' and resid 690 through 709 removed outlier: 4.042A pdb=" N ARG A 696 " --> pdb=" O PRO A 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 432 removed outlier: 3.638A pdb=" N LEU B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) Proline residue: B 426 - end of helix Processing helix chain 'B' and resid 450 through 471 removed outlier: 3.626A pdb=" N ILE B 467 " --> pdb=" O PHE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 517 through 525 removed outlier: 3.733A pdb=" N LYS B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 532 through 538 removed outlier: 3.796A pdb=" N LYS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 545 through 574 removed outlier: 3.653A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 593 Processing helix chain 'B' and resid 606 through 623 Processing helix chain 'B' and resid 634 through 667 removed outlier: 3.660A pdb=" N ALA B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 687 Processing helix chain 'B' and resid 690 through 709 removed outlier: 4.163A pdb=" N ARG B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 432 removed outlier: 3.851A pdb=" N LEU C 416 " --> pdb=" O TRP C 412 " (cutoff:3.500A) Proline residue: C 426 - end of helix Processing helix chain 'C' and resid 450 through 471 removed outlier: 3.803A pdb=" N ILE C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 495 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 507 through 511 Processing helix chain 'C' and resid 517 through 525 removed outlier: 3.960A pdb=" N ILE C 521 " --> pdb=" O SER C 517 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 525 " --> pdb=" O ILE C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 531 Processing helix chain 'C' and resid 532 through 537 Processing helix chain 'C' and resid 538 through 543 Processing helix chain 'C' and resid 545 through 574 removed outlier: 3.679A pdb=" N PHE C 551 " --> pdb=" O ALA C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 Processing helix chain 'C' and resid 606 through 623 Processing helix chain 'C' and resid 634 through 667 removed outlier: 3.642A pdb=" N GLY C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 688 removed outlier: 3.534A pdb=" N ARG C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 709 removed outlier: 4.505A pdb=" N ARG C 696 " --> pdb=" O PRO C 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 432 removed outlier: 3.799A pdb=" N LEU D 416 " --> pdb=" O TRP D 412 " (cutoff:3.500A) Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 450 through 471 removed outlier: 4.251A pdb=" N ASP D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 457 " --> pdb=" O ALA D 453 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 467 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 505 through 506 No H-bonds generated for 'chain 'D' and resid 505 through 506' Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 517 through 525 removed outlier: 3.888A pdb=" N LEU D 523 " --> pdb=" O GLU D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 531 Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 538 through 543 Processing helix chain 'D' and resid 545 through 574 Processing helix chain 'D' and resid 584 through 593 Processing helix chain 'D' and resid 606 through 623 Processing helix chain 'D' and resid 634 through 653 Processing helix chain 'D' and resid 654 through 667 Processing helix chain 'D' and resid 667 through 688 Processing helix chain 'D' and resid 690 through 709 removed outlier: 4.701A pdb=" N ARG D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 700 " --> pdb=" O ARG D 696 " (cutoff:3.500A) 667 hydrogen bonds defined for protein. 1950 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: 6.39 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 9580 1.13 - 1.30: 1520 1.30 - 1.48: 4058 1.48 - 1.65: 4134 1.65 - 1.82: 80 Bond restraints: 19372 Sorted by residual: bond pdb=" N ALA B 527 " pdb=" H ALA B 527 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" CZ2 TRP D 585 " pdb=" HZ2 TRP D 585 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N PHE C 471 " pdb=" H PHE C 471 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 TRP A 412 " pdb=" HD1 TRP A 412 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS B 492 " pdb=" HD2 HIS B 492 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 19367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 29901 2.62 - 5.24: 3865 5.24 - 7.86: 1115 7.86 - 10.49: 15 10.49 - 13.11: 16 Bond angle restraints: 34912 Sorted by residual: angle pdb=" CA ASN B 629 " pdb=" CB ASN B 629 " pdb=" CG ASN B 629 " ideal model delta sigma weight residual 112.60 117.58 -4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" CB HIS D 485 " pdb=" CG HIS D 485 " pdb=" CD2 HIS D 485 " ideal model delta sigma weight residual 131.20 124.83 6.37 1.30e+00 5.92e-01 2.40e+01 angle pdb=" CB HIS B 578 " pdb=" CG HIS B 578 " pdb=" CD2 HIS B 578 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 angle pdb=" CB HIS D 578 " pdb=" CG HIS D 578 " pdb=" CD2 HIS D 578 " ideal model delta sigma weight residual 131.20 124.88 6.32 1.30e+00 5.92e-01 2.36e+01 angle pdb=" CA ASN C 629 " pdb=" CB ASN C 629 " pdb=" CG ASN C 629 " ideal model delta sigma weight residual 112.60 117.39 -4.79 1.00e+00 1.00e+00 2.29e+01 ... (remaining 34907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8550 17.67 - 35.35: 383 35.35 - 53.02: 108 53.02 - 70.69: 78 70.69 - 88.37: 5 Dihedral angle restraints: 9124 sinusoidal: 4760 harmonic: 4364 Sorted by residual: dihedral pdb=" CA LEU A 510 " pdb=" C LEU A 510 " pdb=" N LEU A 511 " pdb=" CA LEU A 511 " ideal model delta harmonic sigma weight residual -180.00 -156.68 -23.32 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA VAL B 476 " pdb=" C VAL B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA PHE B 656 " pdb=" C PHE B 656 " pdb=" N GLY B 657 " pdb=" CA GLY B 657 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 887 0.073 - 0.146: 483 0.146 - 0.218: 100 0.218 - 0.291: 15 0.291 - 0.364: 11 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA SER C 624 " pdb=" N SER C 624 " pdb=" C SER C 624 " pdb=" CB SER C 624 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA SER A 624 " pdb=" N SER A 624 " pdb=" C SER A 624 " pdb=" CB SER A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA SER B 624 " pdb=" N SER B 624 " pdb=" C SER B 624 " pdb=" CB SER B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 1493 not shown) Planarity restraints: 2732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 545 " 0.139 2.00e-02 2.50e+03 6.48e-02 1.26e+02 pdb=" CG TYR A 545 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 545 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR A 545 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 545 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 545 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 545 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 545 " 0.146 2.00e-02 2.50e+03 pdb=" HD1 TYR A 545 " -0.026 2.00e-02 2.50e+03 pdb=" HD2 TYR A 545 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TYR A 545 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 545 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 534 " 0.411 9.50e-02 1.11e+02 1.52e-01 1.15e+02 pdb=" NE ARG A 534 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 534 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 534 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 534 " -0.014 2.00e-02 2.50e+03 pdb="HH11 ARG A 534 " -0.153 2.00e-02 2.50e+03 pdb="HH12 ARG A 534 " 0.072 2.00e-02 2.50e+03 pdb="HH21 ARG A 534 " -0.046 2.00e-02 2.50e+03 pdb="HH22 ARG A 534 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 528 " -0.219 9.50e-02 1.11e+02 9.97e-02 1.09e+02 pdb=" NE ARG B 528 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG B 528 " 0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG B 528 " 0.050 2.00e-02 2.50e+03 pdb=" NH2 ARG B 528 " 0.109 2.00e-02 2.50e+03 pdb="HH11 ARG B 528 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG B 528 " -0.076 2.00e-02 2.50e+03 pdb="HH21 ARG B 528 " -0.127 2.00e-02 2.50e+03 pdb="HH22 ARG B 528 " 0.026 2.00e-02 2.50e+03 ... (remaining 2729 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 986 2.20 - 2.80: 34165 2.80 - 3.40: 52429 3.40 - 4.00: 68827 4.00 - 4.60: 98107 Nonbonded interactions: 254514 Sorted by model distance: nonbonded pdb=" OE2 GLU C 575 " pdb=" HG SER C 636 " model vdw 1.604 2.450 nonbonded pdb=" HG SER D 620 " pdb=" O VAL D 625 " model vdw 1.608 2.450 nonbonded pdb=" HG SER A 620 " pdb=" O VAL A 625 " model vdw 1.609 2.450 nonbonded pdb=" OE2 GLU D 575 " pdb=" HG SER D 636 " model vdw 1.609 2.450 nonbonded pdb=" HG SER B 620 " pdb=" O VAL B 625 " model vdw 1.611 2.450 ... (remaining 254509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.930 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: 0.330 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 40.430 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.013 0.043 9776 Z= 0.822 Angle : 1.701 7.284 13288 Z= 1.180 Chirality : 0.089 0.364 1496 Planarity : 0.016 0.149 1620 Dihedral : 11.670 88.366 3420 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.93 (0.23), residues: 1140 helix: -0.67 (0.15), residues: 880 sheet: None (None), residues: 0 loop : 0.33 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.014 TRP B 585 HIS 0.010 0.002 HIS A 587 PHE 0.075 0.011 PHE C 701 TYR 0.135 0.024 TYR A 545 ARG 0.007 0.001 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.7732 (mmm) cc_final: 0.7418 (ppp) REVERT: A 662 ILE cc_start: 0.7941 (mm) cc_final: 0.7726 (mm) REVERT: A 677 MET cc_start: 0.7953 (tpp) cc_final: 0.7749 (tpp) REVERT: A 690 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: A 701 PHE cc_start: 0.8312 (t80) cc_final: 0.8066 (t80) REVERT: B 457 LEU cc_start: 0.7534 (tp) cc_final: 0.7244 (tt) REVERT: B 540 ASP cc_start: 0.8003 (p0) cc_final: 0.7638 (m-30) REVERT: C 673 TYR cc_start: 0.7713 (t80) cc_final: 0.7370 (t80) REVERT: C 677 MET cc_start: 0.6611 (tpp) cc_final: 0.5941 (ttp) REVERT: C 678 LEU cc_start: 0.8280 (mt) cc_final: 0.7978 (tt) REVERT: C 694 ARG cc_start: 0.7684 (ttt180) cc_final: 0.7196 (ttt180) REVERT: D 462 MET cc_start: 0.7537 (mtp) cc_final: 0.7148 (mtp) REVERT: D 691 ASN cc_start: 0.8232 (t0) cc_final: 0.8018 (t0) REVERT: D 696 ARG cc_start: 0.7274 (mtp180) cc_final: 0.6697 (tmt170) REVERT: D 699 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7222 (mt-10) REVERT: D 703 HIS cc_start: 0.7967 (t-90) cc_final: 0.7710 (t70) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.6386 time to fit residues: 210.2950 Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 HIS A 695 GLN B 573 ASN B 674 HIS C 485 HIS C 691 ASN D 687 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9776 Z= 0.188 Angle : 0.549 5.027 13288 Z= 0.307 Chirality : 0.040 0.145 1496 Planarity : 0.004 0.036 1620 Dihedral : 4.570 18.350 1280 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.57 % Allowed : 4.12 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1140 helix: 0.99 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.65 (0.44), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.005 0.001 HIS C 485 PHE 0.014 0.001 PHE B 701 TYR 0.014 0.002 TYR B 611 ARG 0.003 0.001 ARG D 541 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6557 (tp) REVERT: A 651 MET cc_start: 0.7514 (mmm) cc_final: 0.7197 (ppp) REVERT: A 677 MET cc_start: 0.8092 (tpp) cc_final: 0.7751 (tpt) REVERT: A 679 ARG cc_start: 0.7227 (ttm-80) cc_final: 0.6986 (ttm-80) REVERT: A 690 PRO cc_start: 0.8036 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7350 (tp) cc_final: 0.7056 (tt) REVERT: B 540 ASP cc_start: 0.7842 (p0) cc_final: 0.7615 (m-30) REVERT: B 550 LEU cc_start: 0.8569 (mt) cc_final: 0.8349 (tt) REVERT: C 644 VAL cc_start: 0.9174 (t) cc_final: 0.8957 (t) REVERT: C 677 MET cc_start: 0.6729 (tpp) cc_final: 0.6042 (ttp) REVERT: C 678 LEU cc_start: 0.8333 (mt) cc_final: 0.8057 (tt) REVERT: C 679 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.7094 (tpt-90) REVERT: C 685 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.7237 (mtm110) REVERT: D 462 MET cc_start: 0.7278 (mtp) cc_final: 0.7002 (mtt) REVERT: D 696 ARG cc_start: 0.7362 (mtp180) cc_final: 0.6895 (tmt170) REVERT: D 699 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7148 (mt-10) outliers start: 16 outliers final: 12 residues processed: 223 average time/residue: 0.5137 time to fit residues: 158.4251 Evaluate side-chains 204 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 499 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 0.0770 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 709 ASN C 691 ASN C 709 ASN D 709 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9776 Z= 0.155 Angle : 0.466 4.942 13288 Z= 0.256 Chirality : 0.038 0.149 1496 Planarity : 0.004 0.042 1620 Dihedral : 4.061 16.228 1280 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.08 % Allowed : 6.76 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1140 helix: 1.52 (0.17), residues: 888 sheet: None (None), residues: 0 loop : 0.92 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.004 0.001 HIS C 703 PHE 0.014 0.001 PHE A 656 TYR 0.013 0.001 TYR C 611 ARG 0.003 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 MET cc_start: 0.7540 (mmm) cc_final: 0.7222 (ppp) REVERT: A 679 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6902 (ttm-80) REVERT: A 686 PHE cc_start: 0.7911 (t80) cc_final: 0.7421 (t80) REVERT: A 688 GLN cc_start: 0.8651 (mp10) cc_final: 0.8202 (mp10) REVERT: A 690 PRO cc_start: 0.8064 (Cg_exo) cc_final: 0.7818 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7433 (tp) cc_final: 0.7081 (tt) REVERT: B 540 ASP cc_start: 0.7895 (p0) cc_final: 0.7571 (m-30) REVERT: B 576 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7358 (tt0) REVERT: B 579 MET cc_start: 0.4350 (tmm) cc_final: 0.3972 (tmm) REVERT: B 681 ARG cc_start: 0.6939 (ttp-170) cc_final: 0.6526 (ptp-170) REVERT: B 698 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 462 MET cc_start: 0.7838 (mtt) cc_final: 0.7541 (mtt) REVERT: C 554 MET cc_start: 0.8004 (mmp) cc_final: 0.7532 (mmp) REVERT: C 644 VAL cc_start: 0.9202 (t) cc_final: 0.8978 (t) REVERT: C 677 MET cc_start: 0.6852 (tpp) cc_final: 0.6082 (ttp) REVERT: C 678 LEU cc_start: 0.8288 (mt) cc_final: 0.8064 (tt) REVERT: D 462 MET cc_start: 0.7297 (mtp) cc_final: 0.6997 (mtt) REVERT: D 696 ARG cc_start: 0.7281 (mtp180) cc_final: 0.6798 (tmt170) outliers start: 11 outliers final: 8 residues processed: 202 average time/residue: 0.4859 time to fit residues: 135.8039 Evaluate side-chains 188 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 ASN B 691 ASN C 709 ASN D 709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 9776 Z= 0.310 Angle : 0.524 5.379 13288 Z= 0.292 Chirality : 0.040 0.151 1496 Planarity : 0.004 0.041 1620 Dihedral : 4.069 17.218 1280 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.47 % Allowed : 7.75 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1140 helix: 1.45 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.94 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 585 HIS 0.004 0.001 HIS D 578 PHE 0.019 0.002 PHE B 656 TYR 0.014 0.002 TYR B 611 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.8037 (mttt) cc_final: 0.7207 (tptp) REVERT: A 686 PHE cc_start: 0.8005 (t80) cc_final: 0.7654 (t80) REVERT: A 688 GLN cc_start: 0.8603 (mp10) cc_final: 0.8185 (mp10) REVERT: A 690 PRO cc_start: 0.8306 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7381 (tp) cc_final: 0.7036 (tt) REVERT: B 540 ASP cc_start: 0.7954 (p0) cc_final: 0.7593 (m-30) REVERT: B 576 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7464 (tt0) REVERT: B 579 MET cc_start: 0.4500 (tmm) cc_final: 0.3870 (tmm) REVERT: B 695 GLN cc_start: 0.8213 (mt0) cc_final: 0.7474 (mp10) REVERT: C 644 VAL cc_start: 0.9224 (t) cc_final: 0.9004 (t) REVERT: C 677 MET cc_start: 0.6827 (tpp) cc_final: 0.6155 (ttp) REVERT: C 685 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7371 (mtp85) REVERT: D 462 MET cc_start: 0.7320 (mtp) cc_final: 0.7020 (mtt) REVERT: D 696 ARG cc_start: 0.7374 (mtp180) cc_final: 0.6950 (ttp-170) outliers start: 15 outliers final: 13 residues processed: 186 average time/residue: 0.4993 time to fit residues: 128.4439 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN B 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9776 Z= 0.221 Angle : 0.472 4.608 13288 Z= 0.260 Chirality : 0.038 0.147 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.945 16.762 1280 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 8.43 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.26), residues: 1140 helix: 1.56 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 1.01 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.003 0.001 HIS D 578 PHE 0.017 0.001 PHE A 656 TYR 0.014 0.001 TYR B 611 ARG 0.003 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7931 (mttt) cc_final: 0.7134 (tptp) REVERT: A 686 PHE cc_start: 0.8052 (t80) cc_final: 0.7716 (t80) REVERT: A 688 GLN cc_start: 0.8635 (mp10) cc_final: 0.8256 (mp10) REVERT: A 690 PRO cc_start: 0.8337 (Cg_exo) cc_final: 0.8070 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7489 (tp) cc_final: 0.7088 (tt) REVERT: B 540 ASP cc_start: 0.8022 (p0) cc_final: 0.7581 (m-30) REVERT: B 576 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7567 (tt0) REVERT: B 579 MET cc_start: 0.4394 (tmm) cc_final: 0.3731 (tmm) REVERT: C 644 VAL cc_start: 0.9182 (t) cc_final: 0.8967 (t) REVERT: C 652 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6650 (m-80) REVERT: C 677 MET cc_start: 0.6867 (tpp) cc_final: 0.6239 (ttp) REVERT: D 462 MET cc_start: 0.7303 (mtp) cc_final: 0.6994 (mtt) REVERT: D 696 ARG cc_start: 0.7294 (mtp180) cc_final: 0.6914 (ttp-170) outliers start: 15 outliers final: 10 residues processed: 187 average time/residue: 0.5129 time to fit residues: 133.7011 Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN B 573 ASN C 703 HIS D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9776 Z= 0.185 Angle : 0.453 5.055 13288 Z= 0.248 Chirality : 0.037 0.146 1496 Planarity : 0.004 0.036 1620 Dihedral : 3.825 16.138 1280 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 8.53 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1140 helix: 1.72 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.00 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 568 HIS 0.007 0.001 HIS C 703 PHE 0.017 0.001 PHE A 656 TYR 0.019 0.001 TYR D 493 ARG 0.005 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7920 (mttt) cc_final: 0.7080 (tptp) REVERT: A 686 PHE cc_start: 0.8037 (t80) cc_final: 0.7753 (t80) REVERT: A 688 GLN cc_start: 0.8642 (mp10) cc_final: 0.8258 (mp10) REVERT: A 690 PRO cc_start: 0.8333 (Cg_exo) cc_final: 0.8051 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7479 (tp) cc_final: 0.7075 (tt) REVERT: B 540 ASP cc_start: 0.7974 (p0) cc_final: 0.7546 (m-30) REVERT: B 576 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7585 (tt0) REVERT: B 579 MET cc_start: 0.4408 (tmm) cc_final: 0.3751 (tmm) REVERT: B 685 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7706 (mtm-85) REVERT: C 652 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: C 677 MET cc_start: 0.6964 (tpp) cc_final: 0.6362 (ttp) REVERT: C 695 GLN cc_start: 0.7281 (mp10) cc_final: 0.6946 (mp10) REVERT: D 462 MET cc_start: 0.7294 (mtp) cc_final: 0.6974 (mtt) REVERT: D 696 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6895 (ttp-170) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.5012 time to fit residues: 130.4313 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 695 GLN B 573 ASN C 578 HIS C 703 HIS D 635 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9776 Z= 0.143 Angle : 0.436 4.696 13288 Z= 0.236 Chirality : 0.037 0.145 1496 Planarity : 0.003 0.035 1620 Dihedral : 3.714 16.168 1280 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.57 % Allowed : 8.92 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.26), residues: 1140 helix: 1.87 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.05 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.015 0.001 HIS C 703 PHE 0.020 0.001 PHE A 701 TYR 0.022 0.001 TYR D 493 ARG 0.006 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7913 (mttt) cc_final: 0.7083 (tptp) REVERT: A 688 GLN cc_start: 0.8620 (mp10) cc_final: 0.8250 (mp10) REVERT: A 690 PRO cc_start: 0.8304 (Cg_exo) cc_final: 0.8028 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7434 (tp) cc_final: 0.7027 (tt) REVERT: B 540 ASP cc_start: 0.8000 (p0) cc_final: 0.7534 (m-30) REVERT: B 576 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7577 (tt0) REVERT: B 579 MET cc_start: 0.4538 (tmm) cc_final: 0.3844 (tmm) REVERT: B 685 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7702 (mtm-85) REVERT: C 652 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: C 677 MET cc_start: 0.6910 (tpp) cc_final: 0.6318 (ttp) REVERT: C 679 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7319 (tmt170) REVERT: C 695 GLN cc_start: 0.7273 (mp10) cc_final: 0.6791 (mp10) REVERT: D 462 MET cc_start: 0.7246 (mtp) cc_final: 0.6941 (mtt) REVERT: D 696 ARG cc_start: 0.7212 (mtp180) cc_final: 0.6867 (ttp-170) REVERT: D 698 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7704 (mm-30) outliers start: 16 outliers final: 12 residues processed: 185 average time/residue: 0.4764 time to fit residues: 122.7445 Evaluate side-chains 185 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 573 ASN Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 55 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 97 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN C 578 HIS C 635 ASN D 635 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9776 Z= 0.121 Angle : 0.423 4.436 13288 Z= 0.228 Chirality : 0.036 0.144 1496 Planarity : 0.003 0.035 1620 Dihedral : 3.628 16.150 1280 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.27 % Allowed : 8.73 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.26), residues: 1140 helix: 2.01 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.07 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 568 HIS 0.016 0.001 HIS C 703 PHE 0.017 0.001 PHE A 656 TYR 0.021 0.001 TYR D 493 ARG 0.007 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7903 (mttt) cc_final: 0.7073 (tptp) REVERT: A 688 GLN cc_start: 0.8557 (mp10) cc_final: 0.8213 (mp10) REVERT: A 690 PRO cc_start: 0.8291 (Cg_exo) cc_final: 0.8017 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7392 (tp) cc_final: 0.7012 (tt) REVERT: B 540 ASP cc_start: 0.7995 (p0) cc_final: 0.7510 (m-30) REVERT: B 574 MET cc_start: 0.7673 (mtt) cc_final: 0.7450 (mtm) REVERT: B 576 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7465 (tt0) REVERT: B 579 MET cc_start: 0.4540 (tmm) cc_final: 0.3852 (tmm) REVERT: B 685 ARG cc_start: 0.8127 (mtm180) cc_final: 0.7671 (mtm-85) REVERT: C 652 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.6721 (m-80) REVERT: C 677 MET cc_start: 0.6899 (tpp) cc_final: 0.6324 (ttp) REVERT: C 679 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7323 (tmt170) REVERT: C 695 GLN cc_start: 0.7289 (mp10) cc_final: 0.6972 (mp10) REVERT: D 462 MET cc_start: 0.7220 (mtp) cc_final: 0.6912 (mtt) REVERT: D 696 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6862 (ttp-170) outliers start: 13 outliers final: 11 residues processed: 183 average time/residue: 0.4885 time to fit residues: 123.6536 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 695 GLN B 573 ASN C 578 HIS C 635 ASN C 703 HIS D 635 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9776 Z= 0.213 Angle : 0.462 4.477 13288 Z= 0.253 Chirality : 0.038 0.148 1496 Planarity : 0.004 0.037 1620 Dihedral : 3.678 16.137 1280 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.27 % Allowed : 9.02 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.26), residues: 1140 helix: 1.89 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 1.04 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.008 0.001 HIS C 703 PHE 0.019 0.001 PHE B 656 TYR 0.015 0.001 TYR D 493 ARG 0.006 0.000 ARG C 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7961 (mttt) cc_final: 0.7110 (tptp) REVERT: A 686 PHE cc_start: 0.7991 (t80) cc_final: 0.7686 (t80) REVERT: A 688 GLN cc_start: 0.8566 (mp10) cc_final: 0.8204 (mp10) REVERT: A 690 PRO cc_start: 0.8289 (Cg_exo) cc_final: 0.7978 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7383 (tp) cc_final: 0.7005 (tt) REVERT: B 540 ASP cc_start: 0.8018 (p0) cc_final: 0.7525 (m-30) REVERT: B 574 MET cc_start: 0.7798 (mtt) cc_final: 0.7549 (mtm) REVERT: B 576 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7535 (tt0) REVERT: B 579 MET cc_start: 0.4665 (tmm) cc_final: 0.3951 (tmm) REVERT: C 652 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 677 MET cc_start: 0.6911 (tpp) cc_final: 0.6328 (ttp) REVERT: C 695 GLN cc_start: 0.7268 (mp10) cc_final: 0.6941 (mp10) REVERT: D 462 MET cc_start: 0.7239 (mtp) cc_final: 0.6938 (mtt) REVERT: D 685 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7520 (mtt-85) REVERT: D 696 ARG cc_start: 0.7299 (mtp180) cc_final: 0.6862 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 181 average time/residue: 0.5114 time to fit residues: 126.1298 Evaluate side-chains 187 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN B 573 ASN C 578 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9776 Z= 0.181 Angle : 0.451 5.632 13288 Z= 0.245 Chirality : 0.037 0.146 1496 Planarity : 0.004 0.040 1620 Dihedral : 3.639 16.000 1280 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.27 % Allowed : 9.22 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.26), residues: 1140 helix: 1.92 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 1.08 (0.46), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 568 HIS 0.019 0.001 HIS C 703 PHE 0.018 0.001 PHE A 656 TYR 0.015 0.001 TYR D 493 ARG 0.007 0.000 ARG C 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 LYS cc_start: 0.7947 (mttt) cc_final: 0.7373 (ptmm) REVERT: A 688 GLN cc_start: 0.8636 (mp10) cc_final: 0.8237 (mp10) REVERT: A 690 PRO cc_start: 0.8244 (Cg_exo) cc_final: 0.7950 (Cg_endo) REVERT: B 457 LEU cc_start: 0.7330 (tp) cc_final: 0.6978 (tt) REVERT: B 540 ASP cc_start: 0.8022 (p0) cc_final: 0.7511 (m-30) REVERT: B 574 MET cc_start: 0.7830 (mtt) cc_final: 0.7573 (mtm) REVERT: B 576 GLN cc_start: 0.8347 (tm-30) cc_final: 0.7544 (tt0) REVERT: B 579 MET cc_start: 0.4726 (tmm) cc_final: 0.4000 (tmm) REVERT: C 652 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: C 677 MET cc_start: 0.6908 (tpp) cc_final: 0.6335 (ttp) REVERT: C 695 GLN cc_start: 0.7310 (mp10) cc_final: 0.6907 (mp10) REVERT: D 462 MET cc_start: 0.7220 (mtp) cc_final: 0.6910 (mtt) REVERT: D 685 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7548 (mtt-85) REVERT: D 696 ARG cc_start: 0.7223 (mtp180) cc_final: 0.6855 (ttp-170) outliers start: 13 outliers final: 11 residues processed: 185 average time/residue: 0.5331 time to fit residues: 136.5493 Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 578 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 620 SER Chi-restraints excluded: chain C residue 652 TYR Chi-restraints excluded: chain C residue 703 HIS Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 695 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 695 GLN A 702 GLN C 578 HIS C 635 ASN C 703 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.169065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.111359 restraints weight = 31209.037| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.07 r_work: 0.2913 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9776 Z= 0.177 Angle : 0.447 5.075 13288 Z= 0.244 Chirality : 0.037 0.145 1496 Planarity : 0.004 0.039 1620 Dihedral : 3.610 16.034 1280 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.37 % Allowed : 9.80 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.26), residues: 1140 helix: 1.98 (0.18), residues: 884 sheet: None (None), residues: 0 loop : 1.11 (0.47), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.005 0.001 HIS C 703 PHE 0.018 0.001 PHE A 656 TYR 0.014 0.001 TYR D 493 ARG 0.007 0.000 ARG C 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4581.24 seconds wall clock time: 83 minutes 0.04 seconds (4980.04 seconds total)