Starting phenix.real_space_refine on Tue Feb 11 22:58:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.map" model { file = "/net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dro_27679/02_2025/8dro_27679.cif" } resolution = 4.06 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= 0.049 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 16 5.16 5 C 4270 2.51 5 N 1166 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "C" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 5.54, per 1000 atoms: 0.83 Number of scatterers: 6642 At special positions: 0 Unit cell: (89.08, 100.608, 90.128, 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 16 16.00 O 1190 8.00 N 1166 7.00 C 4270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.57 Conformation dependent library (CDL) restraints added in 907.3 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 32.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.844A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.854A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 4.280A pdb=" N SER B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.532A pdb=" N ASP B 538 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.684A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.637A pdb=" N CYS B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.508A pdb=" N GLY B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.775A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.557A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.634A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.755A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.247A pdb=" N PHE C 611 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.526A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.823A pdb=" N LEU C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.751A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.662A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.763A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 807 Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.965A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 550 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 523 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 552 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737 removed outlier: 6.611A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS C 522 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 573 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 645 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.032A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736 removed outlier: 8.155A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 163 hydrogen bonds defined for protein. 351 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: 1.74 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1247 1.33 - 1.45: 1433 1.45 - 1.57: 4054 1.57 - 1.69: 2 1.69 - 1.81: 20 Bond restraints: 6756 Sorted by residual: bond pdb=" CA HIS C 522 " pdb=" CB HIS C 522 " ideal model delta sigma weight residual 1.533 1.597 -0.064 2.29e-02 1.91e+03 7.69e+00 bond pdb=" C ILE C 508 " pdb=" N PRO C 509 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.20e-02 6.94e+03 5.90e+00 bond pdb=" CB PRO B 509 " pdb=" CG PRO B 509 " ideal model delta sigma weight residual 1.492 1.590 -0.098 5.00e-02 4.00e+02 3.83e+00 bond pdb=" CG LEU B 681 " pdb=" CD1 LEU B 681 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.51e+00 bond pdb=" N GLY C 437 " pdb=" CA GLY C 437 " ideal model delta sigma weight residual 1.445 1.459 -0.014 9.90e-03 1.02e+04 2.04e+00 ... (remaining 6751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8743 1.94 - 3.88: 327 3.88 - 5.82: 61 5.82 - 7.76: 18 7.76 - 9.70: 11 Bond angle restraints: 9160 Sorted by residual: angle pdb=" C ASP B 703 " pdb=" CA ASP B 703 " pdb=" CB ASP B 703 " ideal model delta sigma weight residual 110.01 117.18 -7.17 1.80e+00 3.09e-01 1.59e+01 angle pdb=" N HIS C 522 " pdb=" CA HIS C 522 " pdb=" CB HIS C 522 " ideal model delta sigma weight residual 110.83 117.61 -6.78 1.74e+00 3.30e-01 1.52e+01 angle pdb=" CA LYS B 472 " pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " pdb=" CD LYS B 472 " ideal model delta sigma weight residual 111.30 119.95 -8.65 2.30e+00 1.89e-01 1.41e+01 angle pdb=" CB ARG B 781 " pdb=" CG ARG B 781 " pdb=" CD ARG B 781 " ideal model delta sigma weight residual 111.30 119.83 -8.53 2.30e+00 1.89e-01 1.37e+01 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 3633 16.47 - 32.94: 429 32.94 - 49.41: 97 49.41 - 65.88: 25 65.88 - 82.35: 4 Dihedral angle restraints: 4188 sinusoidal: 1784 harmonic: 2404 Sorted by residual: dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLY B 774 " pdb=" C GLY B 774 " pdb=" N GLU B 775 " pdb=" CA GLU B 775 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR B 679 " pdb=" C THR B 679 " pdb=" N GLN B 680 " pdb=" CA GLN B 680 " ideal model delta harmonic sigma weight residual -180.00 -157.42 -22.58 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 4185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 708 0.040 - 0.080: 298 0.080 - 0.120: 76 0.120 - 0.159: 10 0.159 - 0.199: 6 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CG LEU C 416 " pdb=" CB LEU C 416 " pdb=" CD1 LEU C 416 " pdb=" CD2 LEU C 416 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CG LEU B 491 " pdb=" CB LEU B 491 " pdb=" CD1 LEU B 491 " pdb=" CD2 LEU B 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1095 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 725 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 682 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.53e+00 pdb=" CG PHE B 682 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 682 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 682 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 682 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 682 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 682 " 0.001 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1486 2.79 - 3.32: 6256 3.32 - 3.85: 11128 3.85 - 4.37: 13749 4.37 - 4.90: 21659 Nonbonded interactions: 54278 Sorted by model distance: nonbonded pdb=" O GLN C 560 " pdb=" OG1 THR C 563 " model vdw 2.265 3.040 nonbonded pdb=" O ARG B 492 " pdb=" OG1 THR B 517 " model vdw 2.271 3.040 nonbonded pdb=" O PRO B 777 " pdb=" NZ LYS B 780 " model vdw 2.296 3.120 nonbonded pdb=" OE2 GLU B 493 " pdb=" NZ LYS C 501 " model vdw 2.320 3.120 nonbonded pdb=" O GLN B 560 " pdb=" OG1 THR B 563 " model vdw 2.325 3.040 ... (remaining 54273 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: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.030 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 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 : 0.004 0.098 6756 Z= 0.273 Angle : 0.957 9.695 9160 Z= 0.519 Chirality : 0.046 0.199 1098 Planarity : 0.007 0.093 1156 Dihedral : 15.273 82.350 2612 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.40 % Allowed : 19.44 % Favored : 80.16 % 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: -3.39 (0.27), residues: 810 helix: -2.86 (0.29), residues: 220 sheet: -2.57 (0.54), residues: 90 loop : -1.93 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 475 HIS 0.007 0.001 HIS C 522 PHE 0.039 0.002 PHE B 682 TYR 0.009 0.001 TYR C 668 ARG 0.007 0.001 ARG B 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.730 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: B 453 LEU cc_start: 0.9064 (pp) cc_final: 0.8813 (pp) REVERT: B 519 GLU cc_start: 0.6964 (tp30) cc_final: 0.5596 (tp30) REVERT: B 551 LEU cc_start: 0.8119 (mt) cc_final: 0.6990 (pp) REVERT: B 595 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7358 (mp0) REVERT: B 675 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5844 (mp0) REVERT: B 690 LEU cc_start: 0.8504 (mp) cc_final: 0.8216 (mp) REVERT: B 710 LEU cc_start: 0.7860 (mt) cc_final: 0.7508 (mp) REVERT: B 804 ARG cc_start: 0.3552 (tpt170) cc_final: 0.3153 (tpt-90) REVERT: C 412 THR cc_start: 0.5060 (p) cc_final: 0.4828 (t) REVERT: C 433 PHE cc_start: 0.6844 (t80) cc_final: 0.6068 (t80) REVERT: C 443 PHE cc_start: 0.6891 (m-80) cc_final: 0.5619 (m-80) REVERT: C 503 THR cc_start: 0.7434 (m) cc_final: 0.7172 (m) REVERT: C 744 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5210 (pm20) outliers start: 3 outliers final: 1 residues processed: 236 average time/residue: 0.2419 time to fit residues: 71.0858 Evaluate side-chains 124 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS B 694 HIS C 467 GLN C 650 HIS ** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.168494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.153760 restraints weight = 26429.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.156336 restraints weight = 18064.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.158142 restraints weight = 13244.253| |-----------------------------------------------------------------------------| r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6756 Z= 0.330 Angle : 0.875 9.229 9160 Z= 0.438 Chirality : 0.048 0.226 1098 Planarity : 0.007 0.076 1156 Dihedral : 6.201 23.661 878 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.40 % Allowed : 6.35 % Favored : 93.25 % 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: -3.16 (0.28), residues: 810 helix: -2.85 (0.29), residues: 219 sheet: -2.45 (0.49), residues: 107 loop : -1.62 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 411 HIS 0.007 0.002 HIS C 499 PHE 0.020 0.003 PHE B 682 TYR 0.030 0.003 TYR C 513 ARG 0.007 0.001 ARG C 749 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 LYS cc_start: 0.6385 (mttt) cc_final: 0.5187 (mmmt) REVERT: B 647 TRP cc_start: 0.5254 (p90) cc_final: 0.4831 (p90) REVERT: B 804 ARG cc_start: 0.4814 (tpp-160) cc_final: 0.4281 (tpt-90) REVERT: C 403 ARG cc_start: 0.4237 (OUTLIER) cc_final: 0.3547 (mtm180) REVERT: C 443 PHE cc_start: 0.6577 (m-80) cc_final: 0.5998 (m-80) REVERT: C 473 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6636 (mt-10) REVERT: C 590 MET cc_start: 0.5923 (mmm) cc_final: 0.5547 (mmm) REVERT: C 613 LEU cc_start: 0.4733 (tp) cc_final: 0.4530 (tp) REVERT: C 747 PRO cc_start: 0.3300 (Cg_endo) cc_final: 0.3066 (Cg_exo) outliers start: 3 outliers final: 1 residues processed: 157 average time/residue: 0.2027 time to fit residues: 41.3902 Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 52 optimal weight: 0.4980 chunk 76 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 GLN C 404 GLN C 639 HIS C 711 GLN C 737 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.169629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4567 r_free = 0.4567 target = 0.158903 restraints weight = 26966.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.160276 restraints weight = 20014.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.161297 restraints weight = 15413.927| |-----------------------------------------------------------------------------| r_work (final): 0.4585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6756 Z= 0.231 Angle : 0.727 7.400 9160 Z= 0.367 Chirality : 0.045 0.158 1098 Planarity : 0.006 0.067 1156 Dihedral : 5.855 21.011 878 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -3.04 (0.29), residues: 810 helix: -2.48 (0.32), residues: 210 sheet: -2.79 (0.43), residues: 129 loop : -1.51 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 411 HIS 0.004 0.001 HIS B 614 PHE 0.020 0.002 PHE B 635 TYR 0.020 0.002 TYR C 513 ARG 0.007 0.001 ARG C 600 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.740 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: B 456 ILE cc_start: 0.7860 (tt) cc_final: 0.7644 (tt) REVERT: B 551 LEU cc_start: 0.8043 (mt) cc_final: 0.6250 (pp) REVERT: B 755 ASN cc_start: 0.5097 (t0) cc_final: 0.4561 (m-40) REVERT: B 766 LEU cc_start: 0.4748 (mt) cc_final: 0.4524 (mt) REVERT: C 616 LEU cc_start: 0.8133 (mp) cc_final: 0.7864 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2158 time to fit residues: 42.0270 Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 HIS C 737 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.153608 restraints weight = 27968.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.154729 restraints weight = 23728.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.156192 restraints weight = 17297.772| |-----------------------------------------------------------------------------| r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6756 Z= 0.311 Angle : 0.877 9.919 9160 Z= 0.434 Chirality : 0.049 0.206 1098 Planarity : 0.007 0.066 1156 Dihedral : 6.419 23.217 878 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: -3.23 (0.28), residues: 810 helix: -2.74 (0.32), residues: 213 sheet: -2.33 (0.49), residues: 102 loop : -1.84 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 411 HIS 0.011 0.002 HIS B 499 PHE 0.025 0.003 PHE B 443 TYR 0.023 0.003 TYR C 477 ARG 0.005 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.726 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: B 695 ASN cc_start: 0.4578 (m-40) cc_final: 0.3530 (p0) REVERT: B 755 ASN cc_start: 0.4838 (t0) cc_final: 0.3893 (m-40) REVERT: B 804 ARG cc_start: 0.5385 (tpp-160) cc_final: 0.3389 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1966 time to fit residues: 36.1014 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN B 672 ASN B 758 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.168130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.159314 restraints weight = 28599.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.160046 restraints weight = 23962.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.160366 restraints weight = 16439.559| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6756 Z= 0.193 Angle : 0.719 9.818 9160 Z= 0.357 Chirality : 0.045 0.161 1098 Planarity : 0.005 0.061 1156 Dihedral : 5.726 21.485 878 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.13 % Allowed : 2.38 % Favored : 97.49 % 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: -2.93 (0.29), residues: 810 helix: -2.59 (0.31), residues: 219 sheet: -2.24 (0.47), residues: 112 loop : -1.52 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 411 HIS 0.025 0.002 HIS C 499 PHE 0.013 0.002 PHE B 682 TYR 0.022 0.002 TYR C 477 ARG 0.004 0.000 ARG B 801 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 GLN cc_start: 0.8277 (tm130) cc_final: 0.7809 (tm-30) REVERT: B 695 ASN cc_start: 0.4326 (m-40) cc_final: 0.3837 (p0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1949 time to fit residues: 34.3505 Evaluate side-chains 99 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 77 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.166568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.156972 restraints weight = 26533.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.157750 restraints weight = 24547.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.158314 restraints weight = 16091.483| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 moved from start: 0.7020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6756 Z= 0.193 Angle : 0.698 8.334 9160 Z= 0.344 Chirality : 0.044 0.158 1098 Planarity : 0.006 0.079 1156 Dihedral : 5.682 21.181 878 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -2.83 (0.29), residues: 810 helix: -2.55 (0.32), residues: 213 sheet: -2.23 (0.47), residues: 115 loop : -1.43 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 647 HIS 0.020 0.002 HIS C 499 PHE 0.019 0.002 PHE C 433 TYR 0.023 0.002 TYR C 477 ARG 0.005 0.001 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 GLN cc_start: 0.8369 (tm130) cc_final: 0.7799 (tm-30) REVERT: B 647 TRP cc_start: 0.4314 (p90) cc_final: 0.3528 (p90) REVERT: B 695 ASN cc_start: 0.4116 (m-40) cc_final: 0.3665 (p0) REVERT: B 710 LEU cc_start: 0.6968 (mm) cc_final: 0.6353 (tp) REVERT: B 754 THR cc_start: 0.4251 (t) cc_final: 0.3489 (t) REVERT: B 755 ASN cc_start: 0.4785 (t0) cc_final: 0.4087 (m-40) REVERT: B 760 GLU cc_start: 0.6982 (tt0) cc_final: 0.6726 (tt0) REVERT: C 455 LEU cc_start: 0.8155 (mt) cc_final: 0.7932 (mt) REVERT: C 683 TYR cc_start: 0.6515 (m-10) cc_final: 0.6292 (t80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1965 time to fit residues: 35.2817 Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 0.0270 chunk 53 optimal weight: 0.0670 chunk 73 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 HIS ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.163176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.153645 restraints weight = 27883.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.154070 restraints weight = 24908.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.155164 restraints weight = 18217.993| |-----------------------------------------------------------------------------| r_work (final): 0.4505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6756 Z= 0.251 Angle : 0.792 9.054 9160 Z= 0.391 Chirality : 0.047 0.158 1098 Planarity : 0.006 0.071 1156 Dihedral : 6.081 20.855 878 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -3.17 (0.28), residues: 810 helix: -2.87 (0.30), residues: 212 sheet: -2.16 (0.48), residues: 112 loop : -1.72 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 511 HIS 0.016 0.002 HIS C 499 PHE 0.016 0.002 PHE B 443 TYR 0.018 0.002 TYR C 477 ARG 0.006 0.001 ARG C 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.906 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: B 434 MET cc_start: 0.4383 (mtp) cc_final: 0.4070 (mtp) REVERT: B 473 GLU cc_start: 0.6649 (tp30) cc_final: 0.6382 (tp30) REVERT: B 695 ASN cc_start: 0.4657 (m-40) cc_final: 0.4259 (p0) REVERT: C 683 TYR cc_start: 0.6480 (m-10) cc_final: 0.6261 (t80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2050 time to fit residues: 34.5282 Evaluate side-chains 84 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN B 406 ASN B 467 GLN B 649 ASN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.164992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4521 r_free = 0.4521 target = 0.155638 restraints weight = 28441.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.156786 restraints weight = 22308.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.157682 restraints weight = 17001.258| |-----------------------------------------------------------------------------| r_work (final): 0.4540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5471 moved from start: 0.7914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6756 Z= 0.186 Angle : 0.701 8.380 9160 Z= 0.345 Chirality : 0.044 0.145 1098 Planarity : 0.005 0.064 1156 Dihedral : 5.697 21.545 878 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.13 % Allowed : 0.93 % Favored : 98.94 % 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: -2.92 (0.29), residues: 810 helix: -2.66 (0.33), residues: 205 sheet: -1.98 (0.49), residues: 107 loop : -1.61 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 647 HIS 0.014 0.001 HIS C 499 PHE 0.018 0.002 PHE C 490 TYR 0.016 0.002 TYR B 513 ARG 0.005 0.001 ARG B 801 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.723 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: B 404 GLN cc_start: 0.8436 (tm130) cc_final: 0.7919 (tm-30) outliers start: 1 outliers final: 0 residues processed: 125 average time/residue: 0.2082 time to fit residues: 33.9353 Evaluate side-chains 94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 0.0980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 708 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 GLN C 650 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.163331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.154655 restraints weight = 28971.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.155321 restraints weight = 29484.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.155972 restraints weight = 19189.594| |-----------------------------------------------------------------------------| r_work (final): 0.4521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.8251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.215 Angle : 0.752 7.793 9160 Z= 0.366 Chirality : 0.046 0.216 1098 Planarity : 0.006 0.059 1156 Dihedral : 5.775 20.929 878 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -3.03 (0.28), residues: 810 helix: -2.54 (0.32), residues: 210 sheet: -1.92 (0.51), residues: 97 loop : -1.83 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 475 HIS 0.015 0.001 HIS C 499 PHE 0.020 0.002 PHE C 433 TYR 0.016 0.002 TYR C 477 ARG 0.006 0.001 ARG B 801 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 404 GLN cc_start: 0.8335 (tm130) cc_final: 0.7878 (tm-30) REVERT: C 756 LEU cc_start: 0.6823 (tp) cc_final: 0.6397 (tp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1975 time to fit residues: 33.4091 Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN B 406 ASN B 467 GLN B 576 ASN B 649 ASN B 758 GLN C 650 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.165304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.156322 restraints weight = 28523.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.157581 restraints weight = 22694.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.158823 restraints weight = 15398.335| |-----------------------------------------------------------------------------| r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.8353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6756 Z= 0.173 Angle : 0.716 8.398 9160 Z= 0.345 Chirality : 0.045 0.164 1098 Planarity : 0.005 0.061 1156 Dihedral : 5.487 20.737 878 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.26 % Allowed : 0.40 % Favored : 99.34 % 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: -2.86 (0.28), residues: 810 helix: -2.40 (0.33), residues: 210 sheet: -1.85 (0.51), residues: 97 loop : -1.71 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 511 HIS 0.013 0.001 HIS C 499 PHE 0.016 0.002 PHE C 443 TYR 0.017 0.002 TYR B 513 ARG 0.009 0.001 ARG C 600 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.859 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: B 404 GLN cc_start: 0.8253 (tm130) cc_final: 0.7811 (tm-30) REVERT: B 467 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7364 (pp30) REVERT: C 756 LEU cc_start: 0.6831 (tp) cc_final: 0.6465 (tp) outliers start: 2 outliers final: 0 residues processed: 128 average time/residue: 0.1917 time to fit residues: 32.5659 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN B 406 ASN B 467 GLN ** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.165487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.156031 restraints weight = 27928.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.156905 restraints weight = 22724.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.158425 restraints weight = 16631.719| |-----------------------------------------------------------------------------| r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.8477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6756 Z= 0.168 Angle : 0.694 7.980 9160 Z= 0.336 Chirality : 0.044 0.169 1098 Planarity : 0.005 0.063 1156 Dihedral : 5.409 20.188 878 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.13 % Allowed : 0.26 % Favored : 99.60 % 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: -2.82 (0.28), residues: 810 helix: -2.41 (0.33), residues: 217 sheet: -1.62 (0.54), residues: 97 loop : -1.69 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 511 HIS 0.013 0.001 HIS C 499 PHE 0.015 0.002 PHE C 443 TYR 0.017 0.001 TYR B 513 ARG 0.005 0.000 ARG B 801 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.68 seconds wall clock time: 47 minutes 40.69 seconds (2860.69 seconds total)