Starting phenix.real_space_refine on Thu Jul 24 14:40:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.map" model { file = "/net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rp3_54139/07_2025/9rp3_54139.cif" } resolution = 2.1 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4021 2.51 5 N 1087 2.21 5 O 1207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6349 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3163 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 18, 'TRANS': 379} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3186 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 20, 'TRANS': 380} Chain breaks: 1 Time building chain proxies: 4.77, per 1000 atoms: 0.75 Number of scatterers: 6349 At special positions: 0 Unit cell: (84.216, 80.586, 98.736, 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 34 16.00 O 1207 8.00 N 1087 7.00 C 4021 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: 1.40 Conformation dependent library (CDL) restraints added in 943.0 milliseconds 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1522 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 6 sheets defined 44.2% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.524A pdb=" N GLN A 421 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 422 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 453 Processing helix chain 'A' and resid 479 through 495 Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 552 through 574 Processing helix chain 'A' and resid 583 through 619 removed outlier: 6.124A pdb=" N GLY A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP A 590 " --> pdb=" O GLU A 586 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LYS A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 9.281A pdb=" N SER A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Proline residue: A 612 - end of helix Processing helix chain 'A' and resid 643 through 648 Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.638A pdb=" N THR A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 681 removed outlier: 3.609A pdb=" N THR A 669 " --> pdb=" O GLU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing helix chain 'A' and resid 685 through 690 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 355 through 358 removed outlier: 3.824A pdb=" N ALA B 358 " --> pdb=" O HIS B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 407 through 417 removed outlier: 3.611A pdb=" N LYS B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 3.911A pdb=" N ALA B 422 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 534 through 548 Processing helix chain 'B' and resid 552 through 573 Processing helix chain 'B' and resid 583 through 598 removed outlier: 6.255A pdb=" N GLY B 589 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 619 removed outlier: 4.414A pdb=" N VAL B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Proline residue: B 612 - end of helix Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.671A pdb=" N THR B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 681 removed outlier: 3.774A pdb=" N THR B 669 " --> pdb=" O GLU B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 684 No H-bonds generated for 'chain 'B' and resid 682 through 684' Processing helix chain 'B' and resid 685 through 690 removed outlier: 3.558A pdb=" N ARG B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.269A pdb=" N SER A 374 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 714 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A 693 " --> pdb=" O VAL A 705 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N ARG A 707 " --> pdb=" O HIS A 691 " (cutoff:3.500A) removed outlier: 13.815A pdb=" N HIS A 691 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 692 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 634 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR A 694 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL A 636 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE A 696 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 638 " --> pdb=" O ILE A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 445 removed outlier: 6.525A pdb=" N LYS A 444 " --> pdb=" O ILE A 470 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 469 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ARG A 509 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS A 620 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 343 through 345 Processing sheet with id=AA5, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.581A pdb=" N SER B 374 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA B 714 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET B 693 " --> pdb=" O VAL B 705 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N ARG B 707 " --> pdb=" O HIS B 691 " (cutoff:3.500A) removed outlier: 14.096A pdb=" N HIS B 691 " --> pdb=" O ARG B 707 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LYS B 692 " --> pdb=" O LEU B 632 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU B 634 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N TYR B 694 " --> pdb=" O LEU B 634 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 636 " --> pdb=" O TYR B 694 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ILE B 696 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE B 638 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE B 475 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N SER B 513 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 444 through 445 removed outlier: 6.816A pdb=" N LYS B 444 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 469 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N ARG B 509 " --> pdb=" O VAL B 469 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 858 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: 2.10 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2120 1.34 - 1.46: 1366 1.46 - 1.58: 2932 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6476 Sorted by residual: bond pdb=" N GLU B 319 " pdb=" CA GLU B 319 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.87e+00 bond pdb=" N ARG B 419 " pdb=" CA ARG B 419 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.24e+00 bond pdb=" N ARG A 689 " pdb=" CA ARG A 689 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.35e-02 5.49e+03 4.76e+00 bond pdb=" N ARG B 689 " pdb=" CA ARG B 689 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.35e-02 5.49e+03 4.34e+00 bond pdb=" N LYS A 543 " pdb=" CA LYS A 543 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.21e-02 6.83e+03 4.30e+00 ... (remaining 6471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8630 2.13 - 4.27: 110 4.27 - 6.40: 18 6.40 - 8.53: 6 8.53 - 10.67: 3 Bond angle restraints: 8767 Sorted by residual: angle pdb=" CB LYS A 447 " pdb=" CG LYS A 447 " pdb=" CD LYS A 447 " ideal model delta sigma weight residual 111.30 120.10 -8.80 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CB LYS B 318 " pdb=" CG LYS B 318 " pdb=" CD LYS B 318 " ideal model delta sigma weight residual 111.30 119.61 -8.31 2.30e+00 1.89e-01 1.31e+01 angle pdb=" CB MET A 340 " pdb=" CG MET A 340 " pdb=" SD MET A 340 " ideal model delta sigma weight residual 112.70 123.37 -10.67 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB LYS B 336 " pdb=" CG LYS B 336 " pdb=" CD LYS B 336 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA GLU B 627 " pdb=" CB GLU B 627 " pdb=" CG GLU B 627 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 ... (remaining 8762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 3542 17.68 - 35.35: 321 35.35 - 53.03: 88 53.03 - 70.71: 12 70.71 - 88.38: 9 Dihedral angle restraints: 3972 sinusoidal: 1621 harmonic: 2351 Sorted by residual: dihedral pdb=" CA LEU A 632 " pdb=" C LEU A 632 " pdb=" N ASP A 633 " pdb=" CA ASP A 633 " 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 HIS A 691 " pdb=" C HIS A 691 " pdb=" N LYS A 692 " pdb=" CA LYS A 692 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU B 632 " pdb=" C LEU B 632 " pdb=" N ASP B 633 " pdb=" CA ASP B 633 " ideal model delta harmonic sigma weight residual 180.00 161.31 18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 538 0.027 - 0.054: 259 0.054 - 0.081: 78 0.081 - 0.108: 78 0.108 - 0.135: 24 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA VAL B 397 " pdb=" N VAL B 397 " pdb=" C VAL B 397 " pdb=" CB VAL B 397 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA VAL A 469 " pdb=" N VAL A 469 " pdb=" C VAL A 469 " pdb=" CB VAL A 469 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ARG A 689 " pdb=" N ARG A 689 " pdb=" C ARG A 689 " pdb=" CB ARG A 689 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 974 not shown) Planarity restraints: 1137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 689 " 0.256 9.50e-02 1.11e+02 1.15e-01 8.07e+00 pdb=" NE ARG A 689 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 689 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 689 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 689 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 627 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.42e+00 pdb=" CD GLU B 627 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLU B 627 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 627 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 503 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO B 504 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 504 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 504 " -0.025 5.00e-02 4.00e+02 ... (remaining 1134 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 2800 2.95 - 3.44: 6330 3.44 - 3.93: 10968 3.93 - 4.41: 12400 4.41 - 4.90: 20228 Nonbonded interactions: 52726 Sorted by model distance: nonbonded pdb=" OG SER B 610 " pdb=" NH1 ARG B 707 " model vdw 2.465 3.120 nonbonded pdb=" N GLU B 627 " pdb=" OE1 GLU B 627 " model vdw 2.548 3.120 nonbonded pdb=" O ASP A 442 " pdb=" OD1 ASP A 442 " model vdw 2.566 3.040 nonbonded pdb=" N GLU A 499 " pdb=" OE1 GLU A 499 " model vdw 2.581 3.120 nonbonded pdb=" O LYS B 601 " pdb=" OD2 ASP B 605 " model vdw 2.628 3.040 ... (remaining 52721 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' and resid 314 through 721) } 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: 22.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.050 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.003 0.042 6476 Z= 0.163 Angle : 0.664 10.665 8767 Z= 0.365 Chirality : 0.044 0.135 977 Planarity : 0.006 0.115 1137 Dihedral : 15.011 88.384 2450 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.72 % Allowed : 17.37 % Favored : 81.91 % 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: 1.56 (0.29), residues: 791 helix: 1.33 (0.31), residues: 289 sheet: 1.58 (0.45), residues: 127 loop : 0.77 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 401 HIS 0.004 0.001 HIS B 691 PHE 0.012 0.001 PHE B 607 TYR 0.010 0.001 TYR B 373 ARG 0.006 0.001 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.11703 ( 284) hydrogen bonds : angle 5.73810 ( 858) covalent geometry : bond 0.00328 ( 6476) covalent geometry : angle 0.66432 ( 8767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8789 (tt0) cc_final: 0.8513 (tt0) REVERT: B 501 ASP cc_start: 0.7464 (m-30) cc_final: 0.7044 (m-30) REVERT: B 640 THR cc_start: 0.8606 (p) cc_final: 0.8281 (t) REVERT: B 642 TRP cc_start: 0.8512 (m-10) cc_final: 0.8198 (m-10) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 1.6904 time to fit residues: 158.1595 Evaluate side-chains 72 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 668 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN A 415 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.126073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099897 restraints weight = 9962.318| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.64 r_work: 0.3375 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6476 Z= 0.171 Angle : 0.549 6.173 8767 Z= 0.288 Chirality : 0.044 0.126 977 Planarity : 0.005 0.044 1137 Dihedral : 5.802 90.679 881 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 16.06 % Favored : 81.62 % 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: 1.58 (0.30), residues: 791 helix: 1.34 (0.30), residues: 291 sheet: 1.44 (0.44), residues: 127 loop : 0.84 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.004 0.001 HIS B 691 PHE 0.014 0.002 PHE B 607 TYR 0.008 0.001 TYR B 344 ARG 0.006 0.001 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 284) hydrogen bonds : angle 4.57714 ( 858) covalent geometry : bond 0.00399 ( 6476) covalent geometry : angle 0.54912 ( 8767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8664 (tt0) cc_final: 0.8342 (tt0) REVERT: B 501 ASP cc_start: 0.7403 (m-30) cc_final: 0.6937 (m-30) REVERT: B 525 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: B 640 THR cc_start: 0.8578 (p) cc_final: 0.8262 (t) REVERT: B 642 TRP cc_start: 0.8582 (m-10) cc_final: 0.8231 (m-10) REVERT: B 665 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: B 689 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7601 (mtp180) outliers start: 16 outliers final: 7 residues processed: 91 average time/residue: 2.4101 time to fit residues: 232.9610 Evaluate side-chains 83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.096364 restraints weight = 10073.873| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.64 r_work: 0.3317 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6476 Z= 0.233 Angle : 0.582 6.527 8767 Z= 0.307 Chirality : 0.047 0.134 977 Planarity : 0.005 0.045 1137 Dihedral : 5.727 74.726 879 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.18 % Allowed : 15.77 % Favored : 81.04 % 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: 1.16 (0.29), residues: 791 helix: 1.03 (0.30), residues: 291 sheet: 0.83 (0.44), residues: 121 loop : 0.74 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.006 0.001 HIS A 355 PHE 0.016 0.002 PHE B 607 TYR 0.010 0.001 TYR B 474 ARG 0.006 0.001 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 284) hydrogen bonds : angle 4.61149 ( 858) covalent geometry : bond 0.00545 ( 6476) covalent geometry : angle 0.58152 ( 8767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.671 Fit side-chains REVERT: A 670 GLN cc_start: 0.8702 (tt0) cc_final: 0.8427 (tt0) REVERT: B 472 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: B 501 ASP cc_start: 0.7634 (m-30) cc_final: 0.7280 (m-30) REVERT: B 525 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: B 642 TRP cc_start: 0.8786 (m-10) cc_final: 0.8494 (m-10) REVERT: B 689 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7834 (mtp180) outliers start: 22 outliers final: 7 residues processed: 96 average time/residue: 1.2317 time to fit residues: 124.6904 Evaluate side-chains 85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 36 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.125632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099516 restraints weight = 10171.070| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.67 r_work: 0.3372 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6476 Z= 0.120 Angle : 0.529 11.178 8767 Z= 0.274 Chirality : 0.044 0.134 977 Planarity : 0.004 0.045 1137 Dihedral : 4.880 50.788 877 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.17 % Allowed : 16.93 % Favored : 80.90 % 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: 1.37 (0.29), residues: 791 helix: 1.45 (0.31), residues: 285 sheet: 0.83 (0.45), residues: 121 loop : 0.68 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 389 HIS 0.005 0.001 HIS A 395 PHE 0.017 0.001 PHE B 322 TYR 0.009 0.001 TYR B 373 ARG 0.009 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 284) hydrogen bonds : angle 4.34649 ( 858) covalent geometry : bond 0.00276 ( 6476) covalent geometry : angle 0.52911 ( 8767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.687 Fit side-chains REVERT: A 670 GLN cc_start: 0.8651 (tt0) cc_final: 0.8339 (tt0) REVERT: B 501 ASP cc_start: 0.7354 (m-30) cc_final: 0.7020 (m-30) REVERT: B 525 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: B 642 TRP cc_start: 0.8613 (m-10) cc_final: 0.8221 (m-10) REVERT: B 665 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: B 689 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7699 (mtp180) outliers start: 15 outliers final: 4 residues processed: 86 average time/residue: 1.3085 time to fit residues: 118.0807 Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 52 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.125380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099026 restraints weight = 10111.356| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.68 r_work: 0.3360 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6476 Z= 0.149 Angle : 0.537 10.149 8767 Z= 0.278 Chirality : 0.044 0.144 977 Planarity : 0.005 0.059 1137 Dihedral : 4.886 49.656 877 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.46 % Allowed : 17.08 % Favored : 80.46 % 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: 1.31 (0.29), residues: 791 helix: 1.42 (0.31), residues: 285 sheet: 0.77 (0.45), residues: 121 loop : 0.64 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 389 HIS 0.003 0.001 HIS B 691 PHE 0.012 0.002 PHE B 322 TYR 0.011 0.001 TYR B 373 ARG 0.009 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 284) hydrogen bonds : angle 4.29840 ( 858) covalent geometry : bond 0.00348 ( 6476) covalent geometry : angle 0.53738 ( 8767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.699 Fit side-chains REVERT: A 670 GLN cc_start: 0.8655 (tt0) cc_final: 0.8356 (tt0) REVERT: B 472 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: B 501 ASP cc_start: 0.7344 (m-30) cc_final: 0.6987 (m-30) REVERT: B 525 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 642 TRP cc_start: 0.8646 (m-10) cc_final: 0.8264 (m-10) REVERT: B 665 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7554 (tm-30) REVERT: B 689 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7714 (mtp180) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 1.2173 time to fit residues: 105.1238 Evaluate side-chains 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.124687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.098445 restraints weight = 10095.472| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.66 r_work: 0.3349 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6476 Z= 0.162 Angle : 0.535 9.665 8767 Z= 0.277 Chirality : 0.045 0.139 977 Planarity : 0.005 0.045 1137 Dihedral : 4.905 47.791 877 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 16.64 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 791 helix: 1.41 (0.31), residues: 285 sheet: 0.76 (0.45), residues: 121 loop : 0.59 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 389 HIS 0.003 0.001 HIS B 691 PHE 0.012 0.002 PHE B 607 TYR 0.011 0.001 TYR B 373 ARG 0.008 0.001 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 284) hydrogen bonds : angle 4.30719 ( 858) covalent geometry : bond 0.00379 ( 6476) covalent geometry : angle 0.53504 ( 8767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.651 Fit side-chains REVERT: A 340 MET cc_start: 0.6129 (mmt) cc_final: 0.5811 (mmm) REVERT: A 670 GLN cc_start: 0.8648 (tt0) cc_final: 0.8357 (tt0) REVERT: B 472 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: B 501 ASP cc_start: 0.7294 (m-30) cc_final: 0.6946 (m-30) REVERT: B 525 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: B 642 TRP cc_start: 0.8660 (m-10) cc_final: 0.8265 (m-10) REVERT: B 665 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 689 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7706 (mtp180) outliers start: 18 outliers final: 10 residues processed: 86 average time/residue: 1.1235 time to fit residues: 101.8286 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 43 optimal weight: 0.0170 chunk 78 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.127347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101229 restraints weight = 9965.769| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.67 r_work: 0.3404 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6476 Z= 0.116 Angle : 0.521 9.774 8767 Z= 0.268 Chirality : 0.044 0.139 977 Planarity : 0.004 0.045 1137 Dihedral : 4.794 48.851 877 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.32 % Allowed : 16.50 % Favored : 81.19 % 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: 1.38 (0.29), residues: 791 helix: 1.58 (0.31), residues: 285 sheet: 0.77 (0.45), residues: 121 loop : 0.60 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 389 HIS 0.003 0.001 HIS A 395 PHE 0.010 0.001 PHE B 558 TYR 0.012 0.001 TYR B 373 ARG 0.005 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 284) hydrogen bonds : angle 4.21141 ( 858) covalent geometry : bond 0.00268 ( 6476) covalent geometry : angle 0.52104 ( 8767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.722 Fit side-chains REVERT: A 340 MET cc_start: 0.6079 (mmt) cc_final: 0.5836 (mmm) REVERT: A 670 GLN cc_start: 0.8621 (tt0) cc_final: 0.8304 (tt0) REVERT: B 472 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: B 501 ASP cc_start: 0.7300 (m-30) cc_final: 0.6930 (m-30) REVERT: B 525 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: B 642 TRP cc_start: 0.8585 (m-10) cc_final: 0.8178 (m-10) REVERT: B 665 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: B 689 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7665 (mtp180) outliers start: 16 outliers final: 5 residues processed: 82 average time/residue: 1.1626 time to fit residues: 100.5124 Evaluate side-chains 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 0.2980 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.102465 restraints weight = 10039.558| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.65 r_work: 0.3424 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6476 Z= 0.108 Angle : 0.529 9.649 8767 Z= 0.270 Chirality : 0.043 0.137 977 Planarity : 0.004 0.047 1137 Dihedral : 4.764 49.845 877 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.74 % Allowed : 17.51 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 791 helix: 1.65 (0.31), residues: 285 sheet: 0.78 (0.45), residues: 121 loop : 0.62 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 389 HIS 0.003 0.001 HIS B 691 PHE 0.010 0.001 PHE B 558 TYR 0.012 0.001 TYR B 373 ARG 0.003 0.000 ARG A 678 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 284) hydrogen bonds : angle 4.16211 ( 858) covalent geometry : bond 0.00250 ( 6476) covalent geometry : angle 0.52860 ( 8767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8633 (tt0) cc_final: 0.8343 (tt0) REVERT: B 501 ASP cc_start: 0.7281 (m-30) cc_final: 0.6926 (m-30) REVERT: B 640 THR cc_start: 0.8503 (p) cc_final: 0.8208 (t) REVERT: B 642 TRP cc_start: 0.8555 (m-10) cc_final: 0.8049 (m-10) REVERT: B 665 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: B 689 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7654 (mtp180) outliers start: 12 outliers final: 5 residues processed: 79 average time/residue: 1.5272 time to fit residues: 126.8675 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.126890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100795 restraints weight = 10197.200| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.68 r_work: 0.3394 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6476 Z= 0.138 Angle : 0.547 9.731 8767 Z= 0.279 Chirality : 0.044 0.135 977 Planarity : 0.004 0.045 1137 Dihedral : 4.866 53.016 877 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.45 % Allowed : 18.09 % Favored : 80.46 % 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: 1.42 (0.29), residues: 791 helix: 1.58 (0.31), residues: 285 sheet: 0.81 (0.45), residues: 121 loop : 0.65 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 389 HIS 0.003 0.001 HIS A 404 PHE 0.011 0.002 PHE A 558 TYR 0.012 0.001 TYR B 373 ARG 0.002 0.000 ARG A 419 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 284) hydrogen bonds : angle 4.20046 ( 858) covalent geometry : bond 0.00322 ( 6476) covalent geometry : angle 0.54747 ( 8767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8646 (tt0) cc_final: 0.8412 (tt0) REVERT: B 472 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7233 (pm20) REVERT: B 501 ASP cc_start: 0.7301 (m-30) cc_final: 0.6926 (m-30) REVERT: B 642 TRP cc_start: 0.8609 (m-10) cc_final: 0.8249 (m-10) REVERT: B 665 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: B 689 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7694 (mtp180) outliers start: 10 outliers final: 5 residues processed: 77 average time/residue: 1.3886 time to fit residues: 112.5902 Evaluate side-chains 77 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 689 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 52 optimal weight: 0.0040 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 22 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.2528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.129628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104280 restraints weight = 10126.901| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.66 r_work: 0.3488 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6476 Z= 0.104 Angle : 0.534 10.165 8767 Z= 0.270 Chirality : 0.043 0.136 977 Planarity : 0.004 0.045 1137 Dihedral : 4.727 54.111 877 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.16 % Allowed : 18.81 % Favored : 80.03 % 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: 1.60 (0.30), residues: 791 helix: 1.83 (0.31), residues: 285 sheet: 0.91 (0.45), residues: 121 loop : 0.66 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 389 HIS 0.003 0.001 HIS B 691 PHE 0.011 0.001 PHE B 558 TYR 0.011 0.001 TYR B 373 ARG 0.004 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.03003 ( 284) hydrogen bonds : angle 4.08644 ( 858) covalent geometry : bond 0.00243 ( 6476) covalent geometry : angle 0.53421 ( 8767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1582 Ramachandran restraints generated. 791 Oldfield, 0 Emsley, 791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 583 ASP cc_start: 0.8085 (t70) cc_final: 0.7422 (t0) REVERT: A 670 GLN cc_start: 0.8580 (tt0) cc_final: 0.8300 (tt0) REVERT: B 501 ASP cc_start: 0.7272 (m-30) cc_final: 0.6886 (m-30) REVERT: B 640 THR cc_start: 0.8526 (p) cc_final: 0.8238 (t) REVERT: B 642 TRP cc_start: 0.8506 (m-10) cc_final: 0.8003 (m-10) REVERT: B 665 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: B 683 LYS cc_start: 0.8931 (tppp) cc_final: 0.8704 (mppt) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 2.2080 time to fit residues: 176.8712 Evaluate side-chains 74 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 668 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.128372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102511 restraints weight = 10355.678| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.70 r_work: 0.3427 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6476 Z= 0.124 Angle : 0.544 10.557 8767 Z= 0.275 Chirality : 0.044 0.134 977 Planarity : 0.004 0.045 1137 Dihedral : 4.748 55.134 877 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.72 % Allowed : 19.54 % Favored : 79.74 % 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: 1.57 (0.29), residues: 791 helix: 1.77 (0.31), residues: 285 sheet: 0.93 (0.45), residues: 121 loop : 0.67 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS B 395 PHE 0.011 0.001 PHE B 558 TYR 0.012 0.001 TYR B 373 ARG 0.003 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 284) hydrogen bonds : angle 4.08213 ( 858) covalent geometry : bond 0.00292 ( 6476) covalent geometry : angle 0.54420 ( 8767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8617.56 seconds wall clock time: 156 minutes 29.01 seconds (9389.01 seconds total)