Starting phenix.real_space_refine on Wed Sep 17 06:45:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rp3_54139/09_2025/9rp3_54139.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rp3_54139/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9rp3_54139/09_2025/9rp3_54139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rp3_54139/09_2025/9rp3_54139.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rp3_54139/09_2025/9rp3_54139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rp3_54139/09_2025/9rp3_54139.map" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.85, per 1000 atoms: 0.29 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: 0.49 Conformation dependent library (CDL) restraints added in 420.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.27 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: 0.97 Time building geometry restraints manager: 0.68 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: 2.140 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- 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 : 8.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG A 419 TYR 0.010 0.001 TYR B 373 PHE 0.012 0.001 PHE B 607 TRP 0.014 0.001 TRP B 401 HIS 0.004 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 6476) covalent geometry : angle 0.66432 ( 8767) hydrogen bonds : bond 0.11703 ( 284) hydrogen bonds : angle 5.73810 ( 858) *********************** 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 : 0.264 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: 0.6074 time to fit residues: 56.6272 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 : 0.230 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.127555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101351 restraints weight = 10113.244| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.67 r_work: 0.3399 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0880 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= 0.143 Angle : 0.532 6.073 8767 Z= 0.278 Chirality : 0.044 0.127 977 Planarity : 0.004 0.044 1137 Dihedral : 5.769 94.486 881 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.32 % Allowed : 15.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.30), residues: 791 helix: 1.48 (0.31), residues: 291 sheet: 1.50 (0.44), residues: 127 loop : 0.86 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 419 TYR 0.007 0.001 TYR B 344 PHE 0.012 0.002 PHE B 607 TRP 0.006 0.001 TRP A 401 HIS 0.004 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6476) covalent geometry : angle 0.53218 ( 8767) hydrogen bonds : bond 0.03890 ( 284) hydrogen bonds : angle 4.54412 ( 858) *********************** 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 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8649 (tt0) cc_final: 0.8401 (tt0) REVERT: B 501 ASP cc_start: 0.7380 (m-30) cc_final: 0.6925 (m-30) REVERT: B 640 THR cc_start: 0.8556 (p) cc_final: 0.8227 (t) REVERT: B 642 TRP cc_start: 0.8535 (m-10) cc_final: 0.8153 (m-10) REVERT: B 665 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: B 689 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7538 (mtp180) outliers start: 16 outliers final: 6 residues processed: 92 average time/residue: 0.5725 time to fit residues: 55.3767 Evaluate side-chains 81 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.125034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098884 restraints weight = 10037.023| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.64 r_work: 0.3362 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6476 Z= 0.173 Angle : 0.534 6.557 8767 Z= 0.281 Chirality : 0.045 0.132 977 Planarity : 0.005 0.045 1137 Dihedral : 5.535 80.359 879 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 15.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.29), residues: 791 helix: 1.39 (0.31), residues: 285 sheet: 0.99 (0.45), residues: 121 loop : 0.83 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 419 TYR 0.008 0.001 TYR B 373 PHE 0.013 0.002 PHE B 607 TRP 0.007 0.001 TRP A 401 HIS 0.004 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6476) covalent geometry : angle 0.53428 ( 8767) hydrogen bonds : bond 0.04042 ( 284) hydrogen bonds : angle 4.44133 ( 858) *********************** 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 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8664 (tt0) cc_final: 0.8345 (tt0) REVERT: B 403 ASN cc_start: 0.8101 (t0) cc_final: 0.7699 (m-40) REVERT: B 501 ASP cc_start: 0.7439 (m-30) cc_final: 0.6949 (m-30) REVERT: B 640 THR cc_start: 0.8572 (p) cc_final: 0.8248 (t) REVERT: B 642 TRP cc_start: 0.8598 (m-10) cc_final: 0.8232 (m-10) REVERT: B 665 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: B 689 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7708 (mtp180) outliers start: 18 outliers final: 5 residues processed: 88 average time/residue: 0.5281 time to fit residues: 49.1785 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 : 0.271 ------------------------------------------------------------------------------- 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 665 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 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.126350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.100303 restraints weight = 10072.122| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.65 r_work: 0.3383 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1331 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= 0.127 Angle : 0.502 7.090 8767 Z= 0.264 Chirality : 0.044 0.133 977 Planarity : 0.004 0.045 1137 Dihedral : 4.681 50.324 877 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.17 % Allowed : 16.50 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.30), residues: 791 helix: 1.53 (0.31), residues: 285 sheet: 0.96 (0.45), residues: 121 loop : 0.81 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.009 0.001 TYR B 373 PHE 0.011 0.001 PHE B 607 TRP 0.008 0.001 TRP A 401 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6476) covalent geometry : angle 0.50200 ( 8767) hydrogen bonds : bond 0.03553 ( 284) hydrogen bonds : angle 4.28485 ( 858) *********************** 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 93 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8640 (tt0) cc_final: 0.8357 (tt0) REVERT: B 403 ASN cc_start: 0.8086 (t0) cc_final: 0.7683 (m-40) REVERT: B 501 ASP cc_start: 0.7345 (m-30) cc_final: 0.7004 (m-30) REVERT: B 640 THR cc_start: 0.8546 (p) cc_final: 0.8219 (t) REVERT: B 642 TRP cc_start: 0.8563 (m-10) cc_final: 0.8149 (m-10) REVERT: B 665 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: B 689 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7706 (mtp180) outliers start: 15 outliers final: 7 residues processed: 90 average time/residue: 0.5676 time to fit residues: 53.9342 Evaluate side-chains 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 337 ASP Chi-restraints excluded: chain B residue 452 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 42 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3912 r_free = 0.3912 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.098539 restraints weight = 10201.618| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.67 r_work: 0.3353 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6476 Z= 0.172 Angle : 0.529 7.567 8767 Z= 0.277 Chirality : 0.045 0.139 977 Planarity : 0.004 0.045 1137 Dihedral : 4.773 49.864 877 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.32 % Allowed : 16.21 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.29), residues: 791 helix: 1.42 (0.31), residues: 285 sheet: 0.86 (0.44), residues: 121 loop : 0.73 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 338 TYR 0.010 0.001 TYR B 373 PHE 0.020 0.002 PHE B 322 TRP 0.007 0.001 TRP A 401 HIS 0.004 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 6476) covalent geometry : angle 0.52940 ( 8767) hydrogen bonds : bond 0.03892 ( 284) hydrogen bonds : angle 4.31422 ( 858) *********************** 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 91 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 340 MET cc_start: 0.6106 (mmt) cc_final: 0.5701 (mmm) REVERT: A 670 GLN cc_start: 0.8658 (tt0) cc_final: 0.8369 (tt0) REVERT: B 403 ASN cc_start: 0.8114 (t0) cc_final: 0.7717 (m-40) REVERT: B 446 VAL cc_start: 0.7648 (m) cc_final: 0.7442 (t) REVERT: B 472 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: B 501 ASP cc_start: 0.7354 (m-30) cc_final: 0.7007 (m-30) REVERT: B 640 THR cc_start: 0.8571 (p) cc_final: 0.8241 (t) REVERT: B 642 TRP cc_start: 0.8602 (m-10) cc_final: 0.8196 (m-10) REVERT: B 665 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 689 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7726 (mtp180) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 0.5892 time to fit residues: 53.9025 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 : 0.279 ------------------------------------------------------------------------------- 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 407 MET Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 472 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: 3.9990 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 0.0670 chunk 51 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.126174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099915 restraints weight = 10197.475| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.68 r_work: 0.3378 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1599 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= 0.123 Angle : 0.517 8.648 8767 Z= 0.268 Chirality : 0.044 0.139 977 Planarity : 0.004 0.045 1137 Dihedral : 4.698 49.902 877 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.29), residues: 791 helix: 1.55 (0.31), residues: 285 sheet: 0.87 (0.45), residues: 121 loop : 0.71 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.012 0.001 TYR B 373 PHE 0.018 0.002 PHE B 322 TRP 0.023 0.002 TRP A 389 HIS 0.003 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6476) covalent geometry : angle 0.51700 ( 8767) hydrogen bonds : bond 0.03491 ( 284) hydrogen bonds : angle 4.22596 ( 858) *********************** 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 87 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 340 MET cc_start: 0.5954 (mmt) cc_final: 0.5621 (mmm) REVERT: A 670 GLN cc_start: 0.8637 (tt0) cc_final: 0.8368 (tt0) REVERT: B 403 ASN cc_start: 0.8094 (t0) cc_final: 0.7687 (m-40) REVERT: B 472 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: B 501 ASP cc_start: 0.7318 (m-30) cc_final: 0.6965 (m-30) REVERT: B 640 THR cc_start: 0.8539 (p) cc_final: 0.8214 (t) REVERT: B 642 TRP cc_start: 0.8564 (m-10) cc_final: 0.8146 (m-10) REVERT: B 665 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: B 689 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7694 (mtp180) outliers start: 15 outliers final: 7 residues processed: 82 average time/residue: 0.5907 time to fit residues: 50.9594 Evaluate side-chains 79 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 317 VAL Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 472 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 56 optimal weight: 0.0370 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.128393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102636 restraints weight = 10055.329| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.65 r_work: 0.3458 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6476 Z= 0.108 Angle : 0.504 8.427 8767 Z= 0.260 Chirality : 0.043 0.135 977 Planarity : 0.004 0.045 1137 Dihedral : 4.561 49.287 877 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.32 % Allowed : 16.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.29), residues: 791 helix: 1.69 (0.31), residues: 285 sheet: 0.93 (0.45), residues: 121 loop : 0.71 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.009 0.001 TYR B 373 PHE 0.015 0.001 PHE B 322 TRP 0.019 0.001 TRP A 389 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6476) covalent geometry : angle 0.50402 ( 8767) hydrogen bonds : bond 0.03200 ( 284) hydrogen bonds : angle 4.11031 ( 858) *********************** 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 90 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.229 Fit side-chains REVERT: A 670 GLN cc_start: 0.8630 (tt0) cc_final: 0.8377 (tt0) REVERT: B 403 ASN cc_start: 0.8119 (t0) cc_final: 0.7689 (m-40) REVERT: B 472 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: B 501 ASP cc_start: 0.7321 (m-30) cc_final: 0.6967 (m-30) REVERT: B 601 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8375 (tmtm) REVERT: B 640 THR cc_start: 0.8534 (p) cc_final: 0.8201 (t) REVERT: B 642 TRP cc_start: 0.8487 (m-10) cc_final: 0.8082 (m-10) REVERT: B 665 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: B 689 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7698 (mtp180) outliers start: 16 outliers final: 5 residues processed: 86 average time/residue: 0.6020 time to fit residues: 54.3022 Evaluate side-chains 75 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain B residue 407 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- 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 = 0.3965 r_free = 0.3965 target = 0.128381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102883 restraints weight = 10104.848| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.65 r_work: 0.3465 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1726 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= 0.108 Angle : 0.517 9.056 8767 Z= 0.264 Chirality : 0.043 0.134 977 Planarity : 0.004 0.045 1137 Dihedral : 4.544 48.855 877 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 17.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.30), residues: 791 helix: 1.77 (0.31), residues: 285 sheet: 0.94 (0.45), residues: 121 loop : 0.75 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.011 0.001 TYR B 373 PHE 0.014 0.001 PHE B 322 TRP 0.038 0.002 TRP A 389 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6476) covalent geometry : angle 0.51667 ( 8767) hydrogen bonds : bond 0.03135 ( 284) hydrogen bonds : angle 4.10844 ( 858) *********************** 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 85 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.267 Fit side-chains REVERT: A 352 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7788 (mtt180) REVERT: A 670 GLN cc_start: 0.8641 (tt0) cc_final: 0.8361 (tt0) REVERT: B 403 ASN cc_start: 0.8119 (t0) cc_final: 0.7676 (m-40) REVERT: B 472 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: B 501 ASP cc_start: 0.7328 (m-30) cc_final: 0.6962 (m-30) REVERT: B 601 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8403 (tmtm) REVERT: B 640 THR cc_start: 0.8566 (p) cc_final: 0.8230 (t) REVERT: B 642 TRP cc_start: 0.8500 (m-10) cc_final: 0.8097 (m-10) REVERT: B 665 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 689 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7732 (mtp180) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 0.5610 time to fit residues: 48.4106 Evaluate side-chains 76 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.127474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.101763 restraints weight = 10200.568| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.66 r_work: 0.3411 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1762 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= 0.130 Angle : 0.535 9.396 8767 Z= 0.274 Chirality : 0.044 0.133 977 Planarity : 0.004 0.045 1137 Dihedral : 4.632 48.440 877 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.74 % Allowed : 17.66 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.29), residues: 791 helix: 1.69 (0.31), residues: 285 sheet: 0.91 (0.45), residues: 121 loop : 0.74 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.011 0.001 TYR B 373 PHE 0.012 0.002 PHE B 322 TRP 0.044 0.002 TRP A 389 HIS 0.004 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6476) covalent geometry : angle 0.53514 ( 8767) hydrogen bonds : bond 0.03388 ( 284) hydrogen bonds : angle 4.17061 ( 858) *********************** 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 84 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.268 Fit side-chains REVERT: A 670 GLN cc_start: 0.8580 (tt0) cc_final: 0.8299 (tt0) REVERT: B 403 ASN cc_start: 0.8164 (t0) cc_final: 0.7732 (m-40) REVERT: B 472 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: B 501 ASP cc_start: 0.7293 (m-30) cc_final: 0.6927 (m-30) REVERT: B 601 LYS cc_start: 0.8845 (ttmm) cc_final: 0.8369 (tmtm) REVERT: B 640 THR cc_start: 0.8518 (p) cc_final: 0.8177 (t) REVERT: B 642 TRP cc_start: 0.8510 (m-10) cc_final: 0.8065 (m-10) REVERT: B 665 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: B 689 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7679 (mtp180) outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.5822 time to fit residues: 49.0341 Evaluate side-chains 80 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 397 VAL Chi-restraints excluded: chain B residue 407 MET 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 74 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 0.0070 chunk 73 optimal weight: 0.0270 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.128724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.103238 restraints weight = 10064.838| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.64 r_work: 0.3472 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6476 Z= 0.111 Angle : 0.532 9.923 8767 Z= 0.271 Chirality : 0.043 0.134 977 Planarity : 0.004 0.045 1137 Dihedral : 4.558 48.773 877 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.45 % Allowed : 18.23 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.30), residues: 791 helix: 1.82 (0.31), residues: 285 sheet: 0.92 (0.45), residues: 121 loop : 0.74 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 689 TYR 0.011 0.001 TYR B 373 PHE 0.012 0.001 PHE B 322 TRP 0.011 0.001 TRP A 389 HIS 0.003 0.001 HIS B 691 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6476) covalent geometry : angle 0.53231 ( 8767) hydrogen bonds : bond 0.03109 ( 284) hydrogen bonds : angle 4.11913 ( 858) ********************** 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 82 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 670 GLN cc_start: 0.8588 (tt0) cc_final: 0.8185 (tt0) REVERT: B 403 ASN cc_start: 0.8128 (t0) cc_final: 0.7671 (m-40) REVERT: B 472 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: B 501 ASP cc_start: 0.7305 (m-30) cc_final: 0.6923 (m-30) REVERT: B 601 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8395 (tmtm) REVERT: B 640 THR cc_start: 0.8551 (p) cc_final: 0.8210 (t) REVERT: B 642 TRP cc_start: 0.8469 (m-10) cc_final: 0.8061 (m-10) REVERT: B 665 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: B 689 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7692 (mtp180) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.5582 time to fit residues: 46.5364 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 : 0.268 ------------------------------------------------------------------------------- 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 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 40 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.126773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.100755 restraints weight = 10155.519| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.66 r_work: 0.3394 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1859 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= 0.147 Angle : 0.549 10.358 8767 Z= 0.281 Chirality : 0.044 0.133 977 Planarity : 0.004 0.045 1137 Dihedral : 4.696 47.228 877 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.16 % Allowed : 18.52 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.29), residues: 791 helix: 1.61 (0.31), residues: 285 sheet: 0.87 (0.45), residues: 121 loop : 0.71 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 689 TYR 0.012 0.001 TYR B 373 PHE 0.011 0.002 PHE A 558 TRP 0.007 0.001 TRP A 389 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6476) covalent geometry : angle 0.54865 ( 8767) hydrogen bonds : bond 0.03564 ( 284) hydrogen bonds : angle 4.18272 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3326.11 seconds wall clock time: 57 minutes 18.71 seconds (3438.71 seconds total)